diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
new file mode 100644
index 0000000..32dec1d
--- /dev/null
+++ b/.github/workflows/ci.yaml
@@ -0,0 +1,68 @@
+name: Run CI
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+
+jobs:
+  tests:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 30
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+    name: Run tests
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v5.0.0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6.0.0
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Crossflow and its testing dependencies
+        run: pip install -e .[testing]
+
+      - name: Run test suite
+        run: pytest --cov crossflow --cov-report term-missing --cov-append .
+
+      - name: Coveralls GitHub Action
+        uses: coverallsapp/github-action@v2.3.6
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+
+  docs:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v5.0.0
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v6.0.0
+        with:
+          python-version: 3.13
+      - name: Install python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[docs]
+      - name: Build docs
+        run: cd docs && make
+
+  pre-commit:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v5.0.0
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v6.0.0
+        with:
+          python-version: 3.13
+      - name: Install python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[pre-commit,docs,testing]
+      - name: Run pre-commit
+        run: |
+          pre-commit install
+          pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
deleted file mode 100644
index fd1ea31..0000000
--- a/.github/workflows/python-package.yml
+++ /dev/null
@@ -1,41 +0,0 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
-name: Python package
-
-on:
-  push:
-    branches: [ "master" ]
-  pull_request:
-    branches: [ "master" ]
-
-jobs:
-  build:
-
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ["3.9", "3.10", "3.11"]
-        os: ["ubuntu-latest", "macOS-latest"]
-
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        pytest
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
new file mode 100644
index 0000000..b87f8d5
--- /dev/null
+++ b/.github/workflows/release.yaml
@@ -0,0 +1,140 @@
+
+name: release
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        required: true
+        default: 'x.y.z'
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  checks:
+    name: Version check
+    runs-on: ubuntu-24.04
+    steps:
+    - name: Checkout repository
+      id: repo
+      uses: actions/checkout@v5.0.0
+
+    - name: Set up Python
+      uses: actions/setup-python@v6.0.0
+      with:
+        python-version: 3.13
+
+    - name: Get latest release from pip
+      id: latestreleased
+      run: |
+        PREVIOUS_VERSION=$(python -m pip index versions crossflow | grep "crossflow" | cut -d "(" -f2 | cut -d ")" -f1)
+        echo "pip_tag=$PREVIOUS_VERSION" >> "$GITHUB_OUTPUT"
+        echo $PREVIOUS_VERSION
+
+    - name: version comparison
+      id: compare
+      run: |
+        pip3 install semver
+        output=$(pysemver compare ${{ steps.latestreleased.outputs.pip_tag }} ${{ github.event.inputs.version }})
+        if [ $output -ge 0 ]; then exit 1; fi
+
+  version:
+    name: prepare ${{ github.event.inputs.version }}
+    needs: checks
+    runs-on: ubuntu-24.04
+    steps:
+
+      - name: checkout
+        uses: actions/checkout@v5.0.0
+
+      - name: Change version in repo
+        run: sed -i "s/__version__ =.*/__version__ = \"${{ github.event.inputs.version }}\"/g" crossflow/__init__.py
+
+      - name: send PR
+        id: pr_id
+        uses: peter-evans/create-pull-request@v7.0.8
+        with:
+          commit-message: Update version to ${{ github.event.inputs.version }}
+          branch: version-update
+          title: "Update to version ${{ github.event.inputs.version }}"
+          body: |
+            Update version
+            - Update the __init__.py with new release
+            - Auto-generated by [CI]
+          committer: version-updater <vu.bot@users.noreply.github.com>
+          author: version-updater <vu.bot@users.noreply.github.com>
+          base: main
+          signoff: false
+          draft: false
+
+      - name: auto approve review
+        uses: hmarr/auto-approve-action@v4.0.0
+        with:
+          pull-request-number: ${{ steps.pr_id.outputs.pull-request-number }}
+          review-message: "Auto approved version bump PR"
+          github-token: ${{ secrets.AUTO_PR_MERGE }}
+
+      - name: merge PR
+        run: gh pr merge --merge --delete-branch --auto "${{ steps.pr_id.outputs.pull-request-number }}"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  tag:
+    name: tag release
+    needs: version
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5.0.0
+        with:
+          ref: main
+
+      - name: tag v${{ github.event.inputs.version }}
+        run: |
+          git config user.name github-actions
+          git config user.email github-actions@github.com
+          git tag ${{ github.event.inputs.version }}
+          git push origin tag ${{ github.event.inputs.version }}
+
+  release:
+    name: make github release
+    needs: tag
+    runs-on: ubuntu-24.04
+    steps:
+
+      - name: create release
+        uses: softprops/action-gh-release@v2.3.3
+        with:
+          name: v${{ github.event.inputs.version }}
+          generate_release_notes: true
+          tag_name: ${{ github.event.inputs.version }}
+
+  pypi:
+    name: make pypi release
+    needs: [tag, release]
+    runs-on: ubuntu-24.04
+    steps:
+
+    - name: checkout
+      uses: actions/checkout@v5.0.0
+      with:
+        ref: main
+
+    - name: Set up Python
+      uses: actions/setup-python@v6.0.0
+      with:
+        python-version: 3.13
+
+    - name: Install flit
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flit~=3.9
+
+    - name: Build and publish
+      run: |
+        flit publish
+      env:
+        FLIT_USERNAME: __token__
+        FLIT_PASSWORD:  ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.gitignore b/.gitignore
index 5808f93..b5e4256 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,8 +1,133 @@
+# Byte-compiled / optimized / DLL files
 __pycache__/
-.vscode
-.idea
-*.egg_info/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
 build/
+develop-eggs/
 dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+.pytest_cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/autosummary/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# result and temp file
+*.out
+*.obj
+*.npz
+*.pkl
+*.csv
+Example_output/
+Example/data/*.csv
+
+# profraw files from LLVM? Unclear exactly what triggers this
+# There are reports this comes from LLVM profiling, but also Xcode 9.
+*profraw
+# trajectory file too big
+Example/data/1AKI_prod.trr
+Example/data/1AKI_prod.tpr
+
+# output directories, log file and outputs
+job*
+*.json
+*.err
+*.com
+*.txt
+.idea
+
+# dask
 dask-worker-space
-.ipynb_checkpoints/
+
+# visual studio
+.vscode
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..11ebc11
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,41 @@
+exclude: "^examples/|.*.ipynb"
+repos:
+  - repo: https://github.com/psf/black
+    rev: 25.1.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-executables-have-shebangs
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile=black"]
+
+  - repo: local
+    hooks:
+    - id: pylint
+      language: system
+      types: [file, python]
+      name: pylint
+      description: "This hook runs the pylint static code analyzer"
+      exclude: &exclude_files >
+        (?x)^(
+            docs/.*|
+            examples/.*|
+            tests/.*|
+        )$
+      entry: pylint
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
new file mode 100644
index 0000000..f08a84d
--- /dev/null
+++ b/.readthedocs.yaml
@@ -0,0 +1,19 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+version: 2
+
+build:
+  os: "ubuntu-24.04"
+  tools:
+    python: "3.13"
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+sphinx:
+  # Path to your Sphinx configuration file.
+  configuration: docs/source/conf.py
diff --git a/LICENSE.txt b/LICENSE
old mode 100755
new mode 100644
similarity index 100%
rename from LICENSE.txt
rename to LICENSE
diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100755
index 588f1fd..0000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1,3 +0,0 @@
-
-# Include the license file
-include LICENSE.txt
diff --git a/README.md b/README.md
index 7c098bd..51c2f9f 100644
--- a/README.md
+++ b/README.md
@@ -1,15 +1,21 @@
+[//]: # (Badges)
+[![CodeEntropy CI](https://github.com/CharlieLaughton/crossflow/actions/workflows/ci.yaml/badge.svg)](https://github.com/CharlieLaughton/crossflow/actions/workflows/ci.yaml)
+[![Docs - Status](https://app.readthedocs.org/projects/crossflow/badge/?version=latest)](https://crossflow.readthedocs.io/en/latest/?badge=latest)
+![PyPI - Version](https://img.shields.io/pypi/v/crossflow?logo=pypi&logoColor=white)
+![PyPI - Status](https://img.shields.io/pypi/status/crossflow?logo=pypi&logoColor=white)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/crossflow)
+![PyPI - Total Downloads](https://img.shields.io/pepy/dt/crossflow?logo=pypi&logoColor=white&color=blue)
+![PyPI - Monthly Downloads](https://img.shields.io/pypi/dm/crossflow?logo=pypi&logoColor=white&color=blue)
+[![Coverage Status](https://coveralls.io/repos/github/CharlieLaughton/crossflow/badge.svg?branch=main)](https://coveralls.io/github/CharlieLaughton/crossflow?branch=main)
+[![DOI](https://zenodo.org/badge/802170523.svg)](https://zenodo.org/doi/10.5281/zenodo.12191599)
+
 # Crossflow
 
 A Python-based workflow system.
 
-Crossflow allows you to build and execute complex workflows that chain together 
+Crossflow allows you to build and execute complex workflows that chain together
 command-line driven tools.
 
-For details, see the [Wiki](https://github.com/CharlieLaughton/crossflow/wiki).
-
-### Releases:
-
-[![DOI](https://zenodo.org/badge/802170523.svg)](https://zenodo.org/doi/10.5281/zenodo.12191599)
 
 ### Authors:
 
@@ -17,4 +23,6 @@ Charlie Laughton [charles.laughton@nottingham.ac.uk](mailto:charles.laughton@not
 
 Christian Suess
 
+James Gebbie-Rayet [james.gebbie@stfc.ac.uk](mailto:james.gebbie@stfc.ac.uk)
+
 Sam Cox
diff --git a/crossflow/__init__.py b/crossflow/__init__.py
old mode 100755
new mode 100644
index e69de29..70495fd
--- a/crossflow/__init__.py
+++ b/crossflow/__init__.py
@@ -0,0 +1,8 @@
+"""
+Crossflow
+
+Crossflow allows you to build and execute complex workflows that chain
+together command-line driven tools.
+"""
+
+__version__ = "0.1.4"
diff --git a/crossflow/_version.py b/crossflow/_version.py
deleted file mode 100755
index 2eed5be..0000000
--- a/crossflow/_version.py
+++ /dev/null
@@ -1,4 +0,0 @@
-"""
-_version.py: defines the code version
-"""
-__version__ = "0.1.3"
diff --git a/crossflow/clients.py b/crossflow/clients.py
old mode 100755
new mode 100644
index 84554d8..d1e4044
--- a/crossflow/clients.py
+++ b/crossflow/clients.py
@@ -1,18 +1,23 @@
 """
 Clients.py: thin wrapper over dask client
 """
+
 import glob
 import pickle
 import sys
+
 from dask.distributed import Client as DaskClient
+
 try:
     from collections import Iterable
 except ImportError:
     from collections.abc import Iterable
+
 from dask.distributed import Future
-from .tasks import FunctionTask, SubprocessTask
-from .filehandling import FileHandler
+
 from . import config
+from .filehandling import FileHandler
+from .tasks import FunctionTask, SubprocessTask
 
 
 class Client(DaskClient):
@@ -188,7 +193,7 @@ def submit(self, func, *args, **kwargs):
             newargs = self._futurize(newargs)
 
         if isinstance(func, (SubprocessTask, FunctionTask)):
-            kwargs['pure'] = False
+            kwargs["pure"] = False
             future = super().submit(func.run, *newargs, **kwargs)
             return self._unpack(func, future)
         else:
@@ -224,24 +229,22 @@ def map(self, func, *iterables, **kwargs):
             if isinstance(iterable, (list, tuple)):
                 n_items = len(iterable)
                 if n_items != maxlen:
-                    raise ValueError(
-                        "Error: not all iterables are same length"
-                    )
+                    raise ValueError("Error: not all iterables are same length")
                 its.append(iterable)
             else:
                 its.append([iterable] * maxlen)
 
-        kwargs['pure'] = False
+        kwargs["pure"] = False
         if isinstance(func, (SubprocessTask, FunctionTask)):
             newits = self._filehandlify(its)
             for i, arg in enumerate(newits):
                 newits[i] = self._futurize(arg)
 
-            #futures = super().map(func, *newits, **kwargs)
+            # futures = super().map(func, *newits, **kwargs)
             futures = [super().submit(func, *newit, **kwargs) for newit in zip(*newits)]
             result = [self._unpack(func, future) for future in futures]
         else:
-            #result = super().map(func, *its, **kwargs)
+            # result = super().map(func, *its, **kwargs)
             result = [super().submit(func, *it, **kwargs) for it in zip(*its)]
         if isinstance(result[0], tuple):
             result = self._lt2tl(result)
diff --git a/crossflow/filehandling.py b/crossflow/filehandling.py
old mode 100755
new mode 100644
index fbb992e..e97b714
--- a/crossflow/filehandling.py
+++ b/crossflow/filehandling.py
@@ -5,11 +5,13 @@
 """
 
 import os
-import zlib
 import os.path as op
+import tempfile
 import uuid
+import zlib
+
 import fsspec
-import tempfile
+
 from . import config
 
 """
@@ -58,9 +60,7 @@ class FileHandle(object):
 
     def __init__(self, path, stage_point, must_exist=True):
         if not isinstance(path, (os.PathLike, str, bytes)):
-            raise IOError(
-                f"Error - illegal argument type {type(path)} for {path}"
-            )
+            raise IOError(f"Error - illegal argument type {type(path)} for {path}")
         if must_exist:
             if not os.path.exists(path):
                 raise IOError("Error - no such file")
@@ -75,9 +75,7 @@ def __init__(self, path, stage_point, must_exist=True):
                     self.store = zlib.compress(s.read())
             else:
                 self.staging_path = op.join(stage_point, self.uid)
-                self.store = fsspec.open(
-                    self.staging_path, "wb", compression="bz2"
-                )
+                self.store = fsspec.open(self.staging_path, "wb", compression="bz2")
                 with source as s:
                     with self.store as d:
                         d.write(s.read())
@@ -162,9 +160,7 @@ def write_binary(self, data):
         if self.staging_path is None:
             self.store = compressed_data
         else:
-            self.store = fsspec.open(
-                self.staging_path, "wb", compression="bz2"
-            )
+            self.store = fsspec.open(self.staging_path, "wb", compression="bz2")
             with self.store as s:
                 s.write(data)
             self.store.mode = "rb"
diff --git a/crossflow/tasks.py b/crossflow/tasks.py
index c6208ee..ac823c2 100644
--- a/crossflow/tasks.py
+++ b/crossflow/tasks.py
@@ -2,17 +2,19 @@
 Crossflow tasks: wrappers round subprocess calls and python functions for
 execution on a crossflow cluster
 """
-import re
-import subprocess
-import os
-import os.path as op
-import tempfile
-import shutil
+
 import copy
 import glob
 from math import log10
-from .filehandling import FileHandler
+import os
+import os.path as op
+import re
+import shutil
+import subprocess
+import tempfile
+
 from . import config
+from .filehandling import FileHandler
 
 STDOUT = "STDOUT"
 DEBUGINFO = "DEBUGINFO"
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000..cf24a3d
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,41 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -n -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: all help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext customdefault
+
+## Runs nit-picky and converting warnings into errors to
+## make sure the documentation is properly written
+customdefault:
+	$(SPHINXBUILD) -b html -nW $(ALLSPHINXOPTS) $(BUILDDIR)/html
+
+all: html
+
+clean:
+	rm -r $(BUILDDIR)
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+
+view:
+	xdg-open $(BUILDDIR)/html/index.html
diff --git a/docs/source/clients.rst b/docs/source/clients.rst
new file mode 100644
index 0000000..e52c587
--- /dev/null
+++ b/docs/source/clients.rst
@@ -0,0 +1,69 @@
+Crossflow Clients
+-----------------
+
+The ``crossflow.clients`` sub-package provides a Client through which
+one can execute tasks on distributed resources. At its heart a
+``crossflow.clients.Client()`` is a
+`dask.distributed <https://distributed.dask.org/en/latest/>`_ client,
+and new users are strongly encouraged to read the documentation there to
+understand how Crossflow works.
+
+Creating a crossflow.Client
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+A Crossflow client provides access to a cluster of workers. These may be
+remote machines, or a set of worker processes on the current compute
+resource (see the dask documentation for more details on the many
+different ways a cluster object can be created). The crossflow.Client is
+initialised with the identity of the cluster it will serve:
+
+.. code:: python
+
+   from crossflow.clients import Client
+   from distributed import LocalCluster # Just one way of creating a cluster
+   cluster = LocalCluster()
+   my_client = Client(cluster)
+
+As a shortcut (typically for testing purposes), a local cluster may be
+created on the fly, to serve the Client:
+
+.. code:: python
+
+
+   my_client = Client()
+
+Using a crossflow.Client
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+A crossflow.Task is sent to a crossflow.Client for execution using the
+client’s .submit() or .map() method.
+
+Running a single job:
+
+.. code:: python
+
+
+   output_future, logfile_future = my_client.submit(my_othertool_task, 'input1.dat', 'input2.dat')
+
+Compare with the interactive version above:
+
+1. The outputs (output_future, logfile_future) are now Futures - again,
+   see the dask documentation for more detail, but also notice the
+   difference: dask’s .submit() method always returns a single Future,
+   while crossflow’s one returns one Future per expected output.
+
+Running a set of jobs in parallel:
+
+.. code:: python
+
+
+   xs = ['input1a.dat', 'input1b.dat', 'input1c.dat']
+   ys = ['input2a.dat', 'input2b.dat', 'input2c.dat']
+   output_futures, logfile_futures = my_client.map(my_othertool_task, xs, ys)
+
+In this case the .map() method returns lists of Futures. The individual
+jobs are scheduled to the workers in the compute cluster in whatever way
+is most efficient, if there are enough of them to run all four jobs in
+parallel, they will.
+
+For more details on Crossflow Clients, see :doc:`here <clients_advanced>`
diff --git a/docs/source/clients_advanced.rst b/docs/source/clients_advanced.rst
new file mode 100644
index 0000000..43b6d9b
--- /dev/null
+++ b/docs/source/clients_advanced.rst
@@ -0,0 +1,73 @@
+Advanced Clients
+=================
+
+Here we go into ``crossflow.clients`` in more detail, see
+:doc:`here <clients>` for the basics.
+
+Currently there is only one Crossflow Client. Under the hood, this is
+basically a Dask.distributed client, and for a full understanding of how
+this works please see the Dask.distributed documentation. Here we
+concentrate on some of the extras the Crossflow Client offers.
+
+Transparent file handling
+-------------------------
+
+The Crossflow ``Client`` understands crossflow ``FileHandles`` and
+converts to/from them as required. The only place where some user
+awareness is generally required is in dealing with the outputs returned
+by client ``.submit()`` and ``.map()`` methods. These are
+``concurrent.Futures``, and while they may be passed on to further tasks
+in the workflow as-is, to extract their data locally one must first call
+their ``.result()`` method and then either save the data to a local file
+with the ``FileHandle``\ ’s ``.save()`` method, or, if working
+interactively, maybe view the contents via the ``FileHandle``\ ’s
+``.read_text()`` method:
+
+.. code:: python
+
+   # Submit the job:
+   output = client.submit(my_task, 'input.dat')
+   # Wait for the job to finish and print the output to the screen:
+   print(output.result().read_text())
+
+Multiple return values
+~~~~~~~~~~~~~~~~~~~~~~
+
+The ``Dask.distributed`` client’s ``.submit()`` method always returns a
+single future, even if the function it is executing returns multiple
+values, e.g.:
+
+.. code:: python
+
+   cluster = distributed.LocalCluster()
+   dask_client = distributed.Client(cluster)
+
+   def sumprod(a, b):
+       return a+b, a * b
+
+   result = dask_client.submit(sumprod, 5, 7) # result is a Future for a tuple
+
+In contrast, a Crossflow client returns one future per expected output
+value:
+
+.. code:: python
+
+   cluster = distributed.LocalCluster()
+   crossflow_client = clients.Client(cluster)
+
+   def sumprod(a, b):
+       return a+b, a * b
+
+   sumprod_task = FunctionTask(sumprod)
+   sumprod_task.set_inputs(['a', 'b'])
+   sumprod_task.set_outputs(['sum', 'prod'])
+
+   sum, prod = crossflow_client.submit(sumprod_task, 5, 7) # result is a pair of futures.
+
+The Crossflow client’s ``.map()`` method functions similarly, returning
+one list of Futures per output variable:
+
+.. code:: python
+
+   sums, prods = crossflow_client.map(sumprod_task, [5,6,7], [7,8,9]) # result is a pair of lists of futures.
+   assert len(sums) == 3
diff --git a/docs/source/conf.py b/docs/source/conf.py
new file mode 100644
index 0000000..c787327
--- /dev/null
+++ b/docs/source/conf.py
@@ -0,0 +1,188 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/stable/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
+# Incase the project was not installed
+import os
+import sys
+import time
+
+sys.path.insert(0, os.path.abspath(".."))
+
+# -- Project information -----------------------------------------------------
+
+project = "Crossflow"
+copyright_first_year = "2020"
+copyright_owners = "Charlie Laughton and Christian Suess"
+author = "Charlie Laughton"
+current_year = str(time.localtime().tm_year)
+copyright_year_string = (
+    current_year
+    if current_year == copyright_first_year
+    else f"{copyright_first_year}-{current_year}"
+)
+copyright = f"{copyright_year_string}, {copyright_owners}. All rights reserved"
+
+# The short X.Y version
+version = ""
+# The full version, including alpha/beta/rc tags
+release = ""
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autosummary",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.extlinks",
+    "sphinx_copybutton",
+]
+
+autosummary_generate = True
+napoleon_google_docstring = False
+napoleon_use_param = False
+napoleon_use_ivar = True
+
+# Add any paths that contain templates here, relative to this directory.
+# templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = ".rst"
+
+# The master toctree document.
+master_doc = "index"
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "en"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path .
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "default"
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "furo"
+# html_logo = "images/blaah"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ["_static"]
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "crossflow_doc"
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (
+        master_doc,
+        "Crossflow.tex",
+        "Crossflow Documentation",
+        "Crossflow",
+        "manual",
+    ),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [(master_doc, "Crossflow", "Crossflow Documentation", [author], 1)]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        master_doc,
+        "Crossflow",
+        "Crossflow Documentation",
+        author,
+        "Crossflow",
+        "Crossflow allows you to build and execute complex workflows that chain together command-line driven tools.",
+    ),
+]
+
+
+# -- Extension configuration -------------------------------------------------
+def setup(app):
+    app.add_css_file("custom.css")
diff --git a/docs/source/developer_guide.rst b/docs/source/developer_guide.rst
new file mode 100644
index 0000000..c6edddf
--- /dev/null
+++ b/docs/source/developer_guide.rst
@@ -0,0 +1,136 @@
+Developer Guide
+===============
+
+Crossflow is open-source, and we welcome contributions from the wider community to help improve and extend its functionality. This guide walks you through setting up a development environment, running tests, submitting contributions, and maintaining coding standards.
+
+Getting Started for Developers
+------------------------------
+
+Create a virtual environment::
+
+    python -m venv crossflow-dev
+    source crossflow-dev/bin/activate    # Linux/macOS
+    crossflow-dev\Scripts\activate       # Windows
+
+Clone the repository::
+
+    git clone https://github.com/CharlieLaughton/crossflow.git
+    cd crossflow
+
+Install development dependencies::
+
+    pip install -e .[testing,docs,pre-commit]
+
+Running Tests
+-------------
+
+Run the full test suite::
+
+    pytest -v
+
+Run tests with code coverage::
+
+    pytest --cov crossflow --cov-report=term-missing
+
+Run tests for a specific module::
+
+    pytest crossflow/tests/test_client.py
+
+Run a specific test::
+
+    pytest crossflow/tests/test_client.py::test_subprocess_test_data
+
+Coding Standards
+----------------
+
+We use **pre-commit hooks** to maintain code quality and consistent style. To enable these hooks::
+
+    pre-commit install
+
+This ensures:
+
+- **Formatting** via ``black`` (`psf/black`)
+- **Import sorting** via ``isort`` with the ``black`` profile
+- **Linting** via ``flake8`` with ``flake8-pyproject``
+- **Basic checks** via ``pre-commit-hooks``, including:
+
+  - Detection of large added files
+  - AST validity checks
+  - Case conflict detection
+  - Executable shebang verification
+  - Merge conflict detection
+  - TOML and YAML syntax validation
+
+To skip pre-commit checks for a commit::
+
+    git commit -n
+
+.. note::
+
+    Pull requests must pass all pre-commit checks before being merged.
+
+Continuous Integration (CI)
+---------------------------
+
+Crossflow uses **GitHub Actions** to automatically:
+
+- Run all tests
+- Check coding style
+- Build documentation
+- Validate versioning
+
+Every pull request will trigger these checks to ensure quality and stability.
+
+Building Documentation
+----------------------
+
+Build locally::
+
+    cd docs
+    make html
+
+The generated HTML files will be in ``docs/build/html/``. Open ``index.html`` in your browser to view the documentation.
+
+Edit docs in the following directories:
+
+- ``docs/user_guide/``
+- ``docs/developer_guide/``
+
+Contributing Code
+-----------------
+
+Creating an Issue
+^^^^^^^^^^^^^^^^^
+
+If you encounter bugs or want to request features:
+
+1. Open an issue on GitHub.
+2. Provide a clear description and input files if applicable.
+
+Branching
+^^^^^^^^^
+
+- Never commit directly to ``main``.
+- Create a branch named after the issue::
+
+    git checkout -b 123-fix-something
+
+Pull Requests
+^^^^^^^^^^^^^
+
+1. Make your changes in a branch.
+2. Ensure tests and pre-commit checks pass.
+3. Submit a pull request.
+4. At least one core developer will review it.
+5. Include updated documentation and tests for new code.
+
+Summary
+-------
+
+Full developer setup::
+
+    git clone https://github.com/CharlieLaughton/crossflow.git
+    cd crossflow
+    pip install -e .[testing,docs,pre-commit]
+    pre-commit install
+    pytest --cov crossflow --cov-report=term-missing
diff --git a/docs/source/examples.rst b/docs/source/examples.rst
new file mode 100644
index 0000000..ea449a2
--- /dev/null
+++ b/docs/source/examples.rst
@@ -0,0 +1,45 @@
+Putting it all together: a simple example
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Here we create a ``SubprocessTask`` to reverse the order of the lines in
+a file, submit the job to a local ``Client``, and then retrieve and view
+the result.
+
+.. code:: python
+
+   from crossflow import clients, tasks, filehandling
+   from pathlib import Path
+
+   # Create a short text file:
+   here = Path('.')
+   inp_file = here /'input.txt'
+   with inp_file.open('w') as f:
+       for i in range(10):
+           f.write('line {}\n'.format(i))
+
+   # Create a SubprocessTask that will reverse the lines in a file:
+   reverser = tasks.SubprocessTask('tail -r input > output')
+   reverser.set_inputs(['input'])
+   reverser.set_outputs(['output'])
+
+   # Create a local client to run the job, and submit it:
+   client = clients.Client()
+   output = client.submit(reverser, inp_file)
+
+   # output is a Future; collect its result(), convert this FileHandle object to a file, and list its contents:
+   output_file = here / 'joined.txt'
+   output.result().save(output_file)
+   print(output_file.read_text()) # or: print(output.result().read_text())
+
+::
+
+   line 9
+   line 8
+   line 7
+   line 6
+   line 5
+   line 4
+   line 3
+   line 2
+   line 1
+   line 0
diff --git a/docs/source/filehandles.rst b/docs/source/filehandles.rst
new file mode 100644
index 0000000..b7bd036
--- /dev/null
+++ b/docs/source/filehandles.rst
@@ -0,0 +1,70 @@
+Crossflow FileHandles
+---------------------
+
+Command line tools typically take file *names* as arguments:
+
+.. code:: bash
+
+
+   executable -i input.dat -o output.dat
+
+This has issues if you want to do the computing on a distributed system
+where there is no shared filesystem. Crossflow ``FileHandles`` wrap data
+files as serialisable Python objects that can be safely passed around a
+network. Crossflow ``Tasks`` and ``Clients`` natively understand these
+as the equivalents of the filenames one would use for the equivalent
+command line call.
+
+In normal use, FileHandles are created automatically by ``Tasks`` and/or
+``Clients`` as required, the user just has to extract the required data
+from FileHandles returned by Tasks/Clients.
+
+So for example, in:
+
+.. code:: python
+
+   output_future = client.submit(my_task, 'input.dat')
+   output = output_future.result()
+
+``input.dat`` - the name of a local file - is converted by the client
+into a ``FileHandle`` before being sent for processing, and ``output``
+is a ``FileHandle`` which the user will (probably) want to convert back
+to a conventional file, using one of the methods a ``FileHandle``
+provides.
+
+Methods of crossflow.FileHandles
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The .save() method of a ``crossflow.FileHandle`` creates a conventional
+local file with the object’s contents:
+
+.. code:: python
+
+
+   output.save('output.txt')
+
+In addition, ``crossflow.FileHandles`` follow a limited subset of the
+``pathlib.Path`` API. The file handles themselves are ‘path-like’ and
+can be used in place of paths in many circumstances, e.g.:
+
+.. code:: python
+
+   with open(output) as f:
+       data = f.read()
+
+If your 3rd-party Python library is more picky (e.g. expects paths to be
+strings), then you can use the idiom:
+
+.. code:: python
+
+   result = my_fussy_function(str(output))
+
+In a ``Path``-like manner, ``FileHandles`` have ``.read_binary()`` and
+``.read_text()`` methods, e.g.:
+
+.. code:: python
+
+
+   print(output.read_text()) # prints the contents of output to the screen
+
+For more details on FileHandles, see :doc:`here <filehandles_advanced>`
diff --git a/docs/source/filehandles_advanced.rst b/docs/source/filehandles_advanced.rst
new file mode 100644
index 0000000..ed56217
--- /dev/null
+++ b/docs/source/filehandles_advanced.rst
@@ -0,0 +1,82 @@
+Advanced File Handling
+=======================
+
+Here we go into ``Crossflow.FileHandle`` in more detail, see
+:doc:`here <filehandles>` for the basics.
+
+Crossflow is designed for use on distributed computing clusters, and
+does not require that all the workers can see the same filesystem. To
+achieve this, all input and output files are converted to portable
+objects. Most of this is done behind the scenes by ``crossflow.Tasks``
+and ``crossflow.Clients`` and mostly requires no user intervention, but
+on occasion this is helpful.
+
+Crossflow File Handling basics
+------------------------------
+
+When a ``crossflow.Task`` that takes file names as arguments is run, the
+following takes place;
+
+1. The input file is ‘loaded’ into a ``crossflow.FileHandle`` object.
+2. The objects, along with the function to be evaluated, are sent to the
+   worker process.
+3. The worker unpacks the ``FileHandles`` into suitably-named files in
+   the working directory.
+4. The task function is executed.
+5. Output files are loaded into ``FileHandle`` objects and returned from
+   the worker.
+
+What exactly is meant by ‘loading’ a file can be varied. By default,
+each ``FileHandle`` contains a compressed copy of the data in the file
+it is constructed from. This means quite a lot of data may flow between
+the parent process and the workers, but is normally fast. As an
+alternative, file handling can be configured so that ‘loading’ means
+making a copy of the input file in a place that is accessible to both
+parent process and workers.
+
+Configuring Crossflow to use a shared filesystem for file staging
+-----------------------------------------------------------------
+
+If there is a filesystem that is NFS mounted on all workers, then a
+directory on this filesystem may be configured as a ‘stage_point’ for
+crossflow:
+
+.. code:: python
+
+   import crossflow
+   from crossflow import tasks, clients
+
+   crossflow.set_stage_point('/usr/shared/tmp')
+
+   my_task = tasks.SubprocessTask('cat a b > c')
+   my_task.set_inputs(['a', 'b'])
+   my_task.set_outputs(['c'])
+
+   # Connect to an existing distributed cluster:
+   my_client = client.Client(scheduler_file='scheduler.json')
+
+   # Submit the job. Files pass to/from the workers via copies in /usr/shared/tmp:
+   joined = my_client.submit('file1.txt', 'file2.txt')
+
+Configuring Crossflow to use an S3 bucket for file staging
+----------------------------------------------------------
+
+If you have an S3 bucket that can be visible on all workers, then this
+can be configured as a ‘stage_point’ for crossflow:
+
+.. code:: python
+
+   import crossflow
+   from crossflow import tasks, clients
+
+   crossflow.set_stage_point('s3://groupname.username.crossflowbucket')
+
+   my_task = tasks.SubprocessTask('cat a b > c')
+   my_task.set_inputs(['a', 'b'])
+   my_task.set_outputs(['c'])
+
+   # Connect to an existing distributed cluster:
+   my_client = client.Client(scheduler_file='scheduler.json')
+
+   # Submit the job. Files pass to/from the workers via copies in the s3 bucket:
+   joined = my_client.submit('file1.txt', 'file2.txt')
diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
new file mode 100644
index 0000000..32ee253
--- /dev/null
+++ b/docs/source/getting_started.rst
@@ -0,0 +1,69 @@
+Getting Started
+===============
+
+Requirements
+----------------
+
+* Python >= 3.11
+
+Installation
+----------------
+To install the released version:
+
+.. code-block:: bash
+
+    pip install crossflow
+
+To install the latest development version:
+
+.. code-block:: bash
+
+    git clone https://github.com/CharlieLaughton/crossflow.git
+
+.. code-block:: bash
+
+    cd crossflow
+
+.. code-block:: bash
+
+    pip install .
+
+Crossflow 101
+----------------
+
+An introduction to the fundamentals of Crossflow
+
+Workflows are a common feature of much computational science. In a
+workflow, the work to be done requires more than one piece of software,
+and the output from one becomes the input to the next, in some form of
+chain. Classically one would write a bash script or similar to do the
+job, e.g.:
+
+::
+
+   #!/usr/bin/env bash
+   input_file=input.dat
+   intermediate_file=intermediate.dat
+   result_file=result.dat
+
+   executable1 -i $input_file -o $intermediate_file
+   executable2 -i $intermediate_file -o $result_file
+
+This is OK for basic use but:
+
+-  what if your workflow has loops, conditional executions, etc?
+-  what happens if you want to do things at scale?
+
+Crossflow is designed to make this easier. Key points are:
+
+1. The workflow becomes a Python program, and can make use of all
+   programming workflow constructs (loops, if/then/else, etc.)
+2. To do this, it provides a simple approach to turning command line
+   tools into Python functions - this is ``crossflow.tasks``.
+3. It provides a way to hand the processing of individual workflow steps
+   out to a distributed cluster of workers - this is
+   ``crossflow.clients``.
+4. It provides a way to pass data between these functions without
+   relying on the filesystem - this is ``crossflow.filehandling``.
+
+Here we look at each of these components in turn.
diff --git a/docs/source/index.rst b/docs/source/index.rst
new file mode 100644
index 0000000..5f66bdd
--- /dev/null
+++ b/docs/source/index.rst
@@ -0,0 +1,30 @@
+Welcome to Crossflow's documentation!
+=====================================
+
+Crossflow allows you to build and execute complex workflows that chain together command-line driven tools.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   getting_started
+   tasks
+   clients
+   filehandles
+   examples
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Advanced:
+
+   tasks_advanced
+   clients_advanced
+   filehandles_advanced
+   developer_guide
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/source/tasks.rst b/docs/source/tasks.rst
new file mode 100644
index 0000000..3241ace
--- /dev/null
+++ b/docs/source/tasks.rst
@@ -0,0 +1,80 @@
+Crossflow Tasks
+---------------
+
+The ``crossflow.tasks`` subpackage provides methods to turn tools that
+would usually be used via the command line into Python functions. The
+basic concept is that a tool that is used from the commmand line
+something like:
+
+::
+
+   #!bash
+
+   my_tool -i input.dat -o output.dat
+
+becomes, in Python:
+
+::
+
+   output = my_tool_task(input)
+
+``Where my_tool_task`` is a ``crossflow.SubprocessTask`` for
+``my_tool``, and ``input`` and ``output`` are ‘path-like’ Python objects
+that in some way or other point at a file of data. This might be as
+simple as strings, e.g. “myproject/input.dat”, but can be more complex -
+see crossflow FileHandles later.
+
+Creating a crossflow.SubprocessTask
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is a three step process:
+
+1. The task is created on the basis of a ``template``, a string with a
+   generalised version of the command you wish to execute.
+2. The inputs for the task are specified.
+3. The outputs from the task are specified.
+
+Thus:
+
+::
+
+   #!python
+
+   my_tool_task = crossflow.tasks.SubprocessTask('my_tool -i x.in -o x.out')
+   my_tool_task.set_inputs(['x.in'])
+   my_tool_task.set_outputs(['x.out'])
+
+Note that the names of files used in the template string are arbitrary,
+‘my_tool -i a -o b’ would do just as well, as long as the corresponding
+names (‘a’, ‘b’) were used in .set_inputs() and .set_outputs().
+
+If the tool takes multiple files as inputs, and/or produces multiple
+output files, the process is the same:
+
+::
+
+   #!python
+
+   my_othertool_task = crossflow.tasks.SubprocessTask('my_othertool -x x.in -y y.in -o x.out -l logfile')
+   my_othertool_task.set_inputs(['x.in', 'y.in'])
+   my_othertool_task.set_outputs(['x.out', 'logfile'])
+
+There is no restriction on the order that inputs and outputs are
+specified in the template string, but the resulting task will expect its
+inputs to be provided in the order they are given in .set_inputs() and
+the tuple of outputs the task produces will be in the order they are
+specified in .set_outputs().
+
+For more advanced aspects of ``SubprocessTask`` creation, see :doc:`here <tasks_advanced>`.
+
+Running a crossflow.SubprocessTask
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Although it is primarily expected that tasks will be run via a
+``crossflow.Client``, they can also be executed directly:
+
+::
+
+   #!python
+
+   output, logfile = my_othertool('input1.dat', 'input2.dat')
diff --git a/docs/source/tasks_advanced.rst b/docs/source/tasks_advanced.rst
new file mode 100644
index 0000000..3a5b893
--- /dev/null
+++ b/docs/source/tasks_advanced.rst
@@ -0,0 +1,138 @@
+Advanced Tasks
+===============
+
+Here we go into ``Crossflow.Tasks`` in more detail, see
+:doc:`here <tasks>` for the basics.
+
+SubprocessTasks: More on templates
+----------------------------------
+
+“Cryptic” input and output files
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+``SubprocessTasks`` are instantiated with a template, a generic version
+of the command line that should be executed, e.g.:
+
+.. code:: python
+
+   my_task = SubprocessTask('my_executable -i input.dat -o output.dat')
+   my_task.set_inputs(['input.dat'])
+   my_task.set_outputs(['output.dat'])
+
+Sometimes a command line tool produces an output file whose name is
+hard-wired and so does not appear in the template. As long as you know
+what the name will be, this does not matter. E.g., suppose
+``my_executable`` also always produces a file called ``logfile``:
+
+::
+
+   my_task = SubprocessTask('my_executable -i input.dat -o output.dat')
+   my_task.set_inputs(['input.dat'])
+   my_task.set_outputs(['output.dat', 'logfile'])
+
+The same applies to input files, e.g. if your executable also expects a
+file called ‘config.dat’ to be present, you might write:
+
+::
+
+   my_task = SubprocessTask('my_executable -i input.dat -o output.dat')
+   my_task.set_inputs(['input.dat', 'config.dat'])
+   my_task.set_outputs(['output.dat', 'logfile'])
+
+Input variables that are not filenames
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+By default, all variables are assumed to be the names of input or output
+files, but you can specify string variables (or variables that can be
+represented as strings) by surrounding them by braces (“{}”) in the
+template. E.g.:
+
+::
+
+   tail_task = SubprocessTask('tail -n {n_lines} input.dat > output.dat')
+   tail_task.set_inputs(['input.dat', 'n_lines'])
+   tail_task.set_outputs(['output.dat'])
+
+   last15 = tail_task('data.txt', 15)
+
+Wildcards
+~~~~~~~~~
+
+The template string can contain wildcards ("*" or “?”), the
+corresponding variable (input or output) then becomes a list of values.
+E.g.:
+
+::
+
+   cat_task = SubprocessTask('cat file* > output.dat')
+   cat_task.set_inputs(['file*'])
+   cat_task.set_outputs(['output.dat'])
+   inputs = ['data1', 'data2', 'data3', 'data4']
+
+   output = cat_task(inputs)
+
+SubprocessTasks: Constants
+--------------------------
+
+If some of the inputs to your ``SubprocessTask`` are going to be
+constants over many calls, you can mark them as such, in which case they
+do not appear in the argument list when the task is run. E.g. if a task
+will always use data from a file ‘constant.dat’ you could write:
+
+.. code:: python
+
+   my_task = SubprocessTask('my_executable -i variable.dat -c constants -o output.dat')
+   my_task.set_inputs(['variable.dat', 'constants'])
+   my_task.set_outputs(['output.dat'])
+   my_task.set_constant('constants', 'constant.dat')
+
+   output1 = my_task('input1.dat') # Note 'constant.dat' does not need to be specified
+   output2 = my_task('input2.dat')
+
+FunctionTasks
+-------------
+
+Though the most common reason to use Crossflow is to provide an
+interface to tools usually used from the command line, tasks can also be
+created to wrap conventional Python functions. The most likely scenario
+for this is where the Python function is compute intensive and so needs
+to be executed on a distributed worker, or where it needs to access a
+large unit of data that resides on a worker from a previous computation.
+
+``FunctionTasks`` are instantiated with the Python function they wrap:
+
+.. code:: python
+
+   def mult(x, y):
+       return x * y
+
+   mult_task = FunctionTask(mult)
+   mult_task.set_inputs(['x', 'y'])
+   mult_task.set_outputs('xy')
+
+   result = mult_task(7.5, 8.4)
+
+Debugging Tasks
+---------------
+
+If an attempt to run a task results in an error, by default an exception
+will be raised. If instead you want to be notified about the error, but
+want execution of the script to continue, then you can include the
+pseudo-variable ``crossflow.DEBUGINFO`` in the list of outputs from your
+task:
+
+::
+
+   awk_task = SubprocessTask('awk -f awkscript input.dat > output.dat')
+   awk_task.set_inputs(['awkscript', 'input.dat'])
+   awk_task.set_outputs(['output.dat'])
+
+   # Will raise an exception if awkscript contains errors:
+   output = awk_task('awkscript', 'infile.txt')
+
+   awk_task.set_outputs(['output.dat', crossflow.DEBUGINFO])
+   # Will not raise an exception if awkscript contains errors:
+   output, debuginfo = awk_task('awkscript', 'infile.txt')
+   ...
+   (examine debuginfo to decide what to do)
+   ...
diff --git a/examples/Notebooks/input.txt b/examples/Notebooks/input.txt
deleted file mode 100644
index 27435e1..0000000
--- a/examples/Notebooks/input.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-line 0
-line 1
-line 2
-line 3
-line 4
-line 5
-line 6
-line 7
-line 8
-line 9
diff --git a/examples/README.md b/examples/README.md
index fb5a6c7..4fe9311 100755
--- a/examples/README.md
+++ b/examples/README.md
@@ -1,5 +1,5 @@
 ## Crossflow examples
 
-The **Scripts** folder contains examples of Python scripts that run simple crossflow workflows.. 
+The **scripts** folder contains examples of Python scripts that run simple crossflow workflows..
 
-The **Notebooks** folder contains a number of Jupyter notebooks that illustrate similar workflows, and also includes some more advanced examples.
+The **notebooks** folder contains a number of Jupyter notebooks that illustrate similar workflows, and also includes some more advanced examples.
diff --git a/examples/Notebooks/Amber/Crossflow workflows 101.ipynb b/examples/notebooks/Amber/Crossflow workflows 101.ipynb
similarity index 100%
rename from examples/Notebooks/Amber/Crossflow workflows 101.ipynb
rename to examples/notebooks/Amber/Crossflow workflows 101.ipynb
diff --git a/examples/Notebooks/Amber/README.md b/examples/notebooks/Amber/README.md
similarity index 100%
rename from examples/Notebooks/Amber/README.md
rename to examples/notebooks/Amber/README.md
diff --git a/examples/Notebooks/Amber/dhfr.crd b/examples/notebooks/Amber/dhfr.crd
similarity index 100%
rename from examples/Notebooks/Amber/dhfr.crd
rename to examples/notebooks/Amber/dhfr.crd
diff --git a/examples/Notebooks/Amber/dhfr.prmtop b/examples/notebooks/Amber/dhfr.prmtop
similarity index 100%
rename from examples/Notebooks/Amber/dhfr.prmtop
rename to examples/notebooks/Amber/dhfr.prmtop
diff --git a/examples/Notebooks/Amber/step1.mdin b/examples/notebooks/Amber/step1.mdin
similarity index 100%
rename from examples/Notebooks/Amber/step1.mdin
rename to examples/notebooks/Amber/step1.mdin
diff --git a/examples/Notebooks/Amber/step2.mdin b/examples/notebooks/Amber/step2.mdin
similarity index 100%
rename from examples/Notebooks/Amber/step2.mdin
rename to examples/notebooks/Amber/step2.mdin
diff --git a/examples/Notebooks/Amber/step3.mdin b/examples/notebooks/Amber/step3.mdin
similarity index 100%
rename from examples/Notebooks/Amber/step3.mdin
rename to examples/notebooks/Amber/step3.mdin
diff --git a/examples/Notebooks/Chignolin_unfolding/README b/examples/notebooks/Chignolin_unfolding/README
similarity index 100%
rename from examples/Notebooks/Chignolin_unfolding/README
rename to examples/notebooks/Chignolin_unfolding/README
diff --git a/examples/Notebooks/Chignolin_unfolding/WE_unfolding.py b/examples/notebooks/Chignolin_unfolding/WE_unfolding.py
similarity index 69%
rename from examples/Notebooks/Chignolin_unfolding/WE_unfolding.py
rename to examples/notebooks/Chignolin_unfolding/WE_unfolding.py
index 0cdb0de..1e5a9ec 100644
--- a/examples/Notebooks/Chignolin_unfolding/WE_unfolding.py
+++ b/examples/notebooks/Chignolin_unfolding/WE_unfolding.py
@@ -2,58 +2,62 @@
 # coding: utf-8
 
 # Demonstration Weighted Ensemble Simulation - Chignolin unfolding
-# 
+#
 # This notebook illustrates how you can write a simple Weighted Ensemble simulation workflow using crossflow.
-# 
+#
 # It is assumed that you already have a Dask Distributed cluster up and running - see the ./cluster folder for a recipie to do this on a Condor cluster. Each Dask worker should be on its own GPU node.
-# 
+#
 # The input files are taken from the WESTPA tutorial.
-# 
+#
 # -----
-# 
+#
 # Import required packages:
-# 
+#
+
+import logging
+import time
 
-from crossflow.kernels import SubprocessKernel
-from crossflow.filehandling import FileHandler
-from crossflow.clients import Client
 import mdtraj as mdt
 import numpy as np
-import time
-import logging
 
-logging.basicConfig(filename='we_unfolding.log', level=logging.DEBUG)
+from crossflow.clients import Client
+from crossflow.filehandling import FileHandler
+from crossflow.kernels import SubprocessKernel
+
+logging.basicConfig(filename="we_unfolding.log", level=logging.DEBUG)
 # Convert the starting structure into an Amber .ncrst format file via MDTraj:
 
-ref = mdt.load('common_files/chignolin.pdb')
-ref.save('chignolin.ncrst')
+ref = mdt.load("common_files/chignolin.pdb")
+ref.save("chignolin.ncrst")
 
 # Load the required starting files:
 
 fh = FileHandler()
-mdin = fh.load('common_files/md.in')
-crds = fh.load('chignolin.ncrst')
-prmtop = fh.load('common_files/chignolin.prmtop')
+mdin = fh.load("common_files/md.in")
+crds = fh.load("chignolin.ncrst")
+prmtop = fh.load("common_files/chignolin.prmtop")
 
-# Create a SubprocessKernel that runs pmemd. All we need back are the 
+# Create a SubprocessKernel that runs pmemd. All we need back are the
 # final coordinates.
 
-pmemd = SubprocessKernel('pmemd.cuda -i mdin -c x.inpcrd -p x.prmtop -r x.ncrst -o x.log')
-#pmemd = SubprocessKernel('mpirun pmemd.MPI -i mdin -c x.inpcrd -p x.prmtop -r x.ncrst -o x.log')
-pmemd.set_inputs(['mdin', 'x.inpcrd', 'x.prmtop'])
-pmemd.set_outputs(['x.ncrst'])
-pmemd.set_constant('mdin', mdin)
-pmemd.set_constant('x.prmtop', prmtop)
+pmemd = SubprocessKernel(
+    "pmemd.cuda -i mdin -c x.inpcrd -p x.prmtop -r x.ncrst -o x.log"
+)
+# pmemd = SubprocessKernel('mpirun pmemd.MPI -i mdin -c x.inpcrd -p x.prmtop -r x.ncrst -o x.log')
+pmemd.set_inputs(["mdin", "x.inpcrd", "x.prmtop"])
+pmemd.set_outputs(["x.ncrst"])
+pmemd.set_constant("mdin", mdin)
+pmemd.set_constant("x.prmtop", prmtop)
 
 
 # Create a crossflow client that talks to our dask cluster:
 
-client = Client(scheduler_file='cluster/scheduler.json')
+client = Client(scheduler_file="cluster/scheduler.json")
 
-# We will have a target of 4 simulations per WE bin, and the bins are defined 
-# by RMSD from the starting structure, between 0.05 nm (limit of what is 
-# considered 'native' structure) and 0.40 nm (above which is 'unfolded' 
-# target state), in 0.02 nm increments. We will run the WE simulation for 50 
+# We will have a target of 4 simulations per WE bin, and the bins are defined
+# by RMSD from the starting structure, between 0.05 nm (limit of what is
+# considered 'native' structure) and 0.40 nm (above which is 'unfolded'
+# target state), in 0.02 nm increments. We will run the WE simulation for 50
 # cycles.
 
 n_cycles = 1000
@@ -75,17 +79,17 @@
 # Main loop:
 for c in range(n_cycles):
     # Calculate which bin each restart structure falls in to:
-    t = mdt.load([str(r.result()) for r in restarts], top = str(prmtop))
+    t = mdt.load([str(r.result()) for r in restarts], top=str(prmtop))
     bin_ids = np.digitize(mdt.rmsd(t, ref), bin_edges)
     # Calculate the weight which has reached the final target bin:
     recycled_weight = np.where(bin_ids == target_bin, weights, 0.0).sum()
-    logging.info('Cycle {}: recycled weight={}'.format(c, recycled_weight))
+    logging.info("Cycle {}: recycled weight={}".format(c, recycled_weight))
     recycled_flux.append(recycled_weight)
-    # Recycle any simulations that have reached the target state back to 
+    # Recycle any simulations that have reached the target state back to
     # the starting state:
     restarts = np.where(bin_ids == target_bin, crds, restarts)
     bin_ids = np.where(bin_ids == target_bin, 0, bin_ids)
-    # Assign restart structures to bins and calculate the total weight in 
+    # Assign restart structures to bins and calculate the total weight in
     # each bin:
     bins = {}
     bin_wts = {}
@@ -104,15 +108,17 @@
     walker_wt_max = max(weights)
     now = time.time()
     cycle_time = now - start
-    logging.info('{} walkers in total'.format(len(restarts)))
-    logging.info('{} of {} bins are populated'.format(n_occ, target_bin))
-    logging.info('per-bin minimum non-zero probability: {:8.6f}'.format(bin_wt_min))
-    logging.info('per-bin maximum probability: {:8.6f}'.format(bin_wt_max))
-    logging.info('per-walker minimum non-zero probability: {:8.6f}'.format(walker_wt_min))
-    logging.info('per-walker maximum probability: {:8.6f}'.format(walker_wt_max))
-    logging.info('Time for this cycle: {:8.1f}s'.format(cycle_time))
+    logging.info("{} walkers in total".format(len(restarts)))
+    logging.info("{} of {} bins are populated".format(n_occ, target_bin))
+    logging.info("per-bin minimum non-zero probability: {:8.6f}".format(bin_wt_min))
+    logging.info("per-bin maximum probability: {:8.6f}".format(bin_wt_max))
+    logging.info(
+        "per-walker minimum non-zero probability: {:8.6f}".format(walker_wt_min)
+    )
+    logging.info("per-walker maximum probability: {:8.6f}".format(walker_wt_max))
+    logging.info("Time for this cycle: {:8.1f}s".format(cycle_time))
     start = now
-    # Replicate or cull simulations from each bin to leave n_reps in each, 
+    # Replicate or cull simulations from each bin to leave n_reps in each,
     # then reallocate the total bin weight evenly amongst the structures:
     starting_coordinates = []
     weights = []
@@ -122,5 +128,5 @@
     # Run the next round of simulations:
     restarts = client.map(pmemd, starting_coordinates)
 
-recycled_flux = np.array(recycled_flux) / 20 # flux per picosecond
-np.save('recycled_flux.npy', recycled_flux)
+recycled_flux = np.array(recycled_flux) / 20  # flux per picosecond
+np.save("recycled_flux.npy", recycled_flux)
diff --git a/examples/Notebooks/Chignolin_unfolding/cluster/README b/examples/notebooks/Chignolin_unfolding/cluster/README
similarity index 100%
rename from examples/Notebooks/Chignolin_unfolding/cluster/README
rename to examples/notebooks/Chignolin_unfolding/cluster/README
diff --git a/examples/Notebooks/Chignolin_unfolding/cluster/dask-scheduler.con b/examples/notebooks/Chignolin_unfolding/cluster/dask-scheduler.con
similarity index 100%
rename from examples/Notebooks/Chignolin_unfolding/cluster/dask-scheduler.con
rename to examples/notebooks/Chignolin_unfolding/cluster/dask-scheduler.con
diff --git a/examples/Notebooks/Chignolin_unfolding/cluster/dask-workers.con b/examples/notebooks/Chignolin_unfolding/cluster/dask-workers.con
similarity index 100%
rename from examples/Notebooks/Chignolin_unfolding/cluster/dask-workers.con
rename to examples/notebooks/Chignolin_unfolding/cluster/dask-workers.con
diff --git a/examples/Notebooks/Chignolin_unfolding/common_files/chignolin.pdb b/examples/notebooks/Chignolin_unfolding/common_files/chignolin.pdb
similarity index 100%
rename from examples/Notebooks/Chignolin_unfolding/common_files/chignolin.pdb
rename to examples/notebooks/Chignolin_unfolding/common_files/chignolin.pdb
diff --git a/examples/Notebooks/Chignolin_unfolding/common_files/chignolin.prmtop b/examples/notebooks/Chignolin_unfolding/common_files/chignolin.prmtop
similarity index 100%
rename from examples/Notebooks/Chignolin_unfolding/common_files/chignolin.prmtop
rename to examples/notebooks/Chignolin_unfolding/common_files/chignolin.prmtop
diff --git a/examples/Notebooks/Chignolin_unfolding/common_files/md.in b/examples/notebooks/Chignolin_unfolding/common_files/md.in
similarity index 100%
rename from examples/Notebooks/Chignolin_unfolding/common_files/md.in
rename to examples/notebooks/Chignolin_unfolding/common_files/md.in
diff --git a/examples/Notebooks/Crossflow 101.ipynb b/examples/notebooks/Crossflow 101.ipynb
similarity index 100%
rename from examples/Notebooks/Crossflow 101.ipynb
rename to examples/notebooks/Crossflow 101.ipynb
diff --git a/examples/Notebooks/Gromacs/Crossflow workflows 101.ipynb b/examples/notebooks/Gromacs/Crossflow workflows 101.ipynb
similarity index 100%
rename from examples/Notebooks/Gromacs/Crossflow workflows 101.ipynb
rename to examples/notebooks/Gromacs/Crossflow workflows 101.ipynb
diff --git a/examples/Notebooks/Gromacs/README.md b/examples/notebooks/Gromacs/README.md
similarity index 100%
rename from examples/Notebooks/Gromacs/README.md
rename to examples/notebooks/Gromacs/README.md
diff --git a/examples/Notebooks/Gromacs/bpti.gro b/examples/notebooks/Gromacs/bpti.gro
similarity index 100%
rename from examples/Notebooks/Gromacs/bpti.gro
rename to examples/notebooks/Gromacs/bpti.gro
diff --git a/examples/Notebooks/Gromacs/bpti.top b/examples/notebooks/Gromacs/bpti.top
similarity index 100%
rename from examples/Notebooks/Gromacs/bpti.top
rename to examples/notebooks/Gromacs/bpti.top
diff --git a/examples/Notebooks/Gromacs/em.mdp b/examples/notebooks/Gromacs/em.mdp
similarity index 100%
rename from examples/Notebooks/Gromacs/em.mdp
rename to examples/notebooks/Gromacs/em.mdp
diff --git a/examples/Notebooks/Gromacs/nvt.mdp b/examples/notebooks/Gromacs/nvt.mdp
similarity index 100%
rename from examples/Notebooks/Gromacs/nvt.mdp
rename to examples/notebooks/Gromacs/nvt.mdp
diff --git a/examples/Notebooks/PockDock/README.md b/examples/notebooks/PockDock/README.md
similarity index 100%
rename from examples/Notebooks/PockDock/README.md
rename to examples/notebooks/PockDock/README.md
diff --git a/examples/Notebooks/PockDock/ReverseDocking.ipynb b/examples/notebooks/PockDock/ReverseDocking.ipynb
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rename from examples/Notebooks/PockDock/ReverseDocking.ipynb
rename to examples/notebooks/PockDock/ReverseDocking.ipynb
diff --git a/examples/Notebooks/PockDock/complexes.list b/examples/notebooks/PockDock/complexes.list
similarity index 100%
rename from examples/Notebooks/PockDock/complexes.list
rename to examples/notebooks/PockDock/complexes.list
diff --git a/examples/Notebooks/PockDock/inverse_results.png b/examples/notebooks/PockDock/inverse_results.png
similarity index 100%
rename from examples/Notebooks/PockDock/inverse_results.png
rename to examples/notebooks/PockDock/inverse_results.png
diff --git a/examples/Notebooks/PockDock/local_cluster.sh b/examples/notebooks/PockDock/local_cluster.sh
similarity index 100%
rename from examples/Notebooks/PockDock/local_cluster.sh
rename to examples/notebooks/PockDock/local_cluster.sh
diff --git a/examples/Notebooks/PockDock/pockdock.ipynb b/examples/notebooks/PockDock/pockdock.ipynb
similarity index 100%
rename from examples/Notebooks/PockDock/pockdock.ipynb
rename to examples/notebooks/PockDock/pockdock.ipynb
diff --git a/examples/Notebooks/PockDock/prz.pdb b/examples/notebooks/PockDock/prz.pdb
similarity index 100%
rename from examples/Notebooks/PockDock/prz.pdb
rename to examples/notebooks/PockDock/prz.pdb
diff --git a/examples/Notebooks/PockDock/prz.pdbqt b/examples/notebooks/PockDock/prz.pdbqt
similarity index 100%
rename from examples/Notebooks/PockDock/prz.pdbqt
rename to examples/notebooks/PockDock/prz.pdbqt
diff --git a/examples/Notebooks/PockDock/receptors/1afq_receptor.pdbqt b/examples/notebooks/PockDock/receptors/1afq_receptor.pdbqt
similarity index 100%
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similarity index 100%
rename from examples/Notebooks/PockDock/receptors/3h9j_receptor.pdbqt
rename to examples/notebooks/PockDock/receptors/3h9j_receptor.pdbqt
diff --git a/examples/Notebooks/PockDock/receptors/3hl7_receptor.pdbqt b/examples/notebooks/PockDock/receptors/3hl7_receptor.pdbqt
similarity index 100%
rename from examples/Notebooks/PockDock/receptors/3hl7_receptor.pdbqt
rename to examples/notebooks/PockDock/receptors/3hl7_receptor.pdbqt
diff --git a/examples/Notebooks/PockDock/receptors/3hl8_receptor.pdbqt b/examples/notebooks/PockDock/receptors/3hl8_receptor.pdbqt
similarity index 100%
rename from examples/Notebooks/PockDock/receptors/3hl8_receptor.pdbqt
rename to examples/notebooks/PockDock/receptors/3hl8_receptor.pdbqt
diff --git a/examples/Notebooks/PockDock/receptors/3hok_receptor.pdbqt b/examples/notebooks/PockDock/receptors/3hok_receptor.pdbqt
similarity index 100%
rename from examples/Notebooks/PockDock/receptors/3hok_receptor.pdbqt
rename to examples/notebooks/PockDock/receptors/3hok_receptor.pdbqt
diff --git a/examples/Notebooks/PockDock/receptors/3hqp_receptor.pdbqt b/examples/notebooks/PockDock/receptors/3hqp_receptor.pdbqt
similarity index 100%
rename from examples/Notebooks/PockDock/receptors/3hqp_receptor.pdbqt
rename to examples/notebooks/PockDock/receptors/3hqp_receptor.pdbqt
diff --git a/examples/Notebooks/PockDock/receptors/3hzt_receptor.pdbqt b/examples/notebooks/PockDock/receptors/3hzt_receptor.pdbqt
similarity index 100%
rename from examples/Notebooks/PockDock/receptors/3hzt_receptor.pdbqt
rename to examples/notebooks/PockDock/receptors/3hzt_receptor.pdbqt
diff --git a/examples/Notebooks/PockDock/receptors/3ip0_receptor.pdbqt b/examples/notebooks/PockDock/receptors/3ip0_receptor.pdbqt
similarity index 100%
rename from examples/Notebooks/PockDock/receptors/3ip0_receptor.pdbqt
rename to examples/notebooks/PockDock/receptors/3ip0_receptor.pdbqt
diff --git a/examples/Notebooks/PockDock/receptors/3ixj_receptor.pdbqt b/examples/notebooks/PockDock/receptors/3ixj_receptor.pdbqt
similarity index 100%
rename from examples/Notebooks/PockDock/receptors/3ixj_receptor.pdbqt
rename to examples/notebooks/PockDock/receptors/3ixj_receptor.pdbqt
diff --git a/examples/Notebooks/PockDock/receptors/3lth_receptor.pdbqt b/examples/notebooks/PockDock/receptors/3lth_receptor.pdbqt
similarity index 100%
rename from examples/Notebooks/PockDock/receptors/3lth_receptor.pdbqt
rename to examples/notebooks/PockDock/receptors/3lth_receptor.pdbqt
diff --git a/examples/Notebooks/README.md b/examples/notebooks/README.md
similarity index 100%
rename from examples/Notebooks/README.md
rename to examples/notebooks/README.md
diff --git a/examples/Notebooks/Simple workflow.ipynb b/examples/notebooks/Simple workflow.ipynb
similarity index 100%
rename from examples/Notebooks/Simple workflow.ipynb
rename to examples/notebooks/Simple workflow.ipynb
diff --git a/examples/Scripts/README.md b/examples/scripts/README.md
similarity index 100%
rename from examples/Scripts/README.md
rename to examples/scripts/README.md
diff --git a/examples/Scripts/Slurm_GPU/dask-mig-worker b/examples/scripts/Slurm_GPU/dask-mig-worker
similarity index 100%
rename from examples/Scripts/Slurm_GPU/dask-mig-worker
rename to examples/scripts/Slurm_GPU/dask-mig-worker
diff --git a/examples/Scripts/Slurm_GPU/slurm_example.sh b/examples/scripts/Slurm_GPU/slurm_example.sh
similarity index 100%
rename from examples/Scripts/Slurm_GPU/slurm_example.sh
rename to examples/scripts/Slurm_GPU/slurm_example.sh
diff --git a/examples/Scripts/example1.py b/examples/scripts/example1.py
similarity index 66%
rename from examples/Scripts/example1.py
rename to examples/scripts/example1.py
index 89d7b38..15c37d2 100644
--- a/examples/Scripts/example1.py
+++ b/examples/scripts/example1.py
@@ -3,20 +3,21 @@
 # Basic example of how to create tasks, load input data, and
 # run locally (without using a client)
 #
-from crossflow import tasks
 from pathlib import Path
 
+from crossflow import tasks
+
 # Create two short text files:
-here = Path('.')
-file1 = here / 'file1.txt'
-file1.write_text('content\n')
-file2 = here / 'file2.txt'
-file2.write_text('more content\n')
+here = Path(".")
+file1 = here / "file1.txt"
+file1.write_text("content\n")
+file2 = here / "file2.txt"
+file2.write_text("more content\n")
 
 # Create a Subprocesstask that will join input files together:
-joiner = tasks.SubprocessTask('cat * > output')
-joiner.set_inputs(['*'])
-joiner.set_outputs(['output'])
+joiner = tasks.SubprocessTask("cat * > output")
+joiner.set_inputs(["*"])
+joiner.set_outputs(["output"])
 
 # The task expects an arbitrary number of input files, so put the inputs
 # into a list, and then call the task:
@@ -24,6 +25,6 @@
 joined = joiner(inputs)
 
 # Save the output FileHandle object as a file, and list its contents:
-output = here / 'joined.txt'
+output = here / "joined.txt"
 joined.save(output)
 print(output.read_text())
diff --git a/examples/Scripts/example2.py b/examples/scripts/example2.py
similarity index 76%
rename from examples/Scripts/example2.py
rename to examples/scripts/example2.py
index 8e46fb6..fbeda73 100644
--- a/examples/Scripts/example2.py
+++ b/examples/scripts/example2.py
@@ -6,22 +6,23 @@
 # the associated client, this part of the process must be done in
 # __main__
 #
-from crossflow import clients, tasks
 from pathlib import Path
 
+from crossflow import clients, tasks
+
 
 def run(client):
     # Create two short text files:
-    here = Path('.')
-    input_file1 = here / 'file1.txt'
-    input_file1.write_text('content\n')
-    input_file2 = here / 'file2.txt'
-    input_file2.write_text('more content\n')
+    here = Path(".")
+    input_file1 = here / "file1.txt"
+    input_file1.write_text("content\n")
+    input_file2 = here / "file2.txt"
+    input_file2.write_text("more content\n")
 
     # Create a Subprocesstask that will join input files together:
-    joiner = tasks.SubprocessTask('cat * > output')
-    joiner.set_inputs(['*'])
-    joiner.set_outputs(['output'])
+    joiner = tasks.SubprocessTask("cat * > output")
+    joiner.set_inputs(["*"])
+    joiner.set_outputs(["output"])
 
     # The task expects an arbitrary number of input files, so put the inputs
     # into a list:
@@ -35,12 +36,12 @@ def run(client):
     output_filehandle = output.result()
 
     # Save the output FileHandle object as a file, and list its contents:
-    output_file = here / 'joined.txt'
+    output_file = here / "joined.txt"
     output_filehandle.save(output_file)
     return output_file
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     # Create a local compute cluster and the client to serve it:
     client = clients.Client()
     output_file = run(client)
diff --git a/examples/Scripts/example3.py b/examples/scripts/example3.py
similarity index 71%
rename from examples/Scripts/example3.py
rename to examples/scripts/example3.py
index 9a979c4..6c7346a 100644
--- a/examples/Scripts/example3.py
+++ b/examples/scripts/example3.py
@@ -6,32 +6,33 @@
 # A large text file is split into a number of separate ones, each of these
 # has its lines reversed (last to first), and then the chunks are recombined.
 #
-from crossflow import clients, tasks
 from pathlib import Path
 
+from crossflow import clients, tasks
+
 
 def run(client):
     # Create the initial text file:
-    here = Path('.')
-    input_file = here / 'input.txt'
-    with input_file.open('w') as f:
+    here = Path(".")
+    input_file = here / "input.txt"
+    with input_file.open("w") as f:
         for i in range(50):
-            f.write('line {}\n'.format(i))
+            f.write("line {}\n".format(i))
 
     # Create a SubprocessTask that will split up the input file:
-    splitter = tasks.SubprocessTask('split -l 10 input.txt')
-    splitter.set_inputs(['input.txt'])
-    splitter.set_outputs(['xaa', 'xab', 'xac', 'xad', 'xae'])
+    splitter = tasks.SubprocessTask("split -l 10 input.txt")
+    splitter.set_inputs(["input.txt"])
+    splitter.set_outputs(["xaa", "xab", "xac", "xad", "xae"])
 
     # Create a SubprocessTask to reverse the order of the lines in a file:
-    reverser = tasks.SubprocessTask('tail -r input > output')
-    reverser.set_inputs(['input'])
-    reverser.set_outputs(['output'])
+    reverser = tasks.SubprocessTask("tail -r input > output")
+    reverser.set_inputs(["input"])
+    reverser.set_outputs(["output"])
 
     # Create a Subprocesstask that will join input files together:
-    joiner = tasks.SubprocessTask('cat * > output')
-    joiner.set_inputs(['*'])
-    joiner.set_outputs(['output'])
+    joiner = tasks.SubprocessTask("cat * > output")
+    joiner.set_inputs(["*"])
+    joiner.set_outputs(["output"])
 
     # Here is the workflow, using .submit() and .map() methods.
     # First split the file into pieces:
@@ -49,12 +50,12 @@ def run(client):
     output_filehandle = output.result()
 
     # Save the output FileHandle object as a file, and list its contents:
-    output_file = here / 'processed.txt'
+    output_file = here / "processed.txt"
     output_filehandle.save(output_file)
     return output_file
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     # Create a local compute cluster and the client to serve it:
     client = clients.Client()
     output_file = run(client)
diff --git a/pyproject.toml b/pyproject.toml
index c9315a3..223f60c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,97 @@
 [build-system]
-requires = ["setuptools", "wheel"]
-build-backend = "setuptools.build_meta"
-[tool.pytest.ini_options]
-pythonpath = [
-  "."
+# Build the package with [flit](https://flit.readthedocs.io)
+requires = ["flit_core >=3.4,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+# See https://www.python.org/dev/peps/pep-0621/
+name = "crossflow"
+dynamic = ["version"]
+description = "Crossflow allows you to build and execute complex workflows that chain together command-line driven tools."
+authors = [
+    {name = "Charlie Laughton", email = "charles.laughton@nottingham.ac.uk"},
+    {name = "Christian Suess", email = "christian.suess@nottingham.ac.uk"},
+    {name = "James Gebbie-Rayet", email = "james.gebbie@stfc.ac.uk"},
+    {name = "Sam Cox", email = "sam.cox@hdruk.ac.uk"},
 ]
+readme = "README.md"
+license = { file = "LICENSE" }
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Natural Language :: English",
+    "Development Status :: 3 - Alpha"
+]
+keywords = ["hpc", "workflows", "molecular dynamics"]
+requires-python = ">=3.11"
+dependencies = [
+    "dask",
+    "distributed",
+    "fsspec",
+]
+
+[project.urls]
+Homepage = "https://"
+Repository = "https://"
+Documentation = "https://"
+
+[project.optional-dependencies]
+testing = [
+    "pytest==8.2.2",
+    "pytest-cov==5.0.0",
+    "pytest-sugar==1.0.0"
+]
+
+pre-commit = [
+    "pre-commit==3.7.1",
+    "pylint==3.2.5"
+]
+docs = [
+    "sphinx",
+    "sphinx_rtd_theme",
+    "sphinxcontrib-contentui",
+    "sphinxcontrib-details-directive",
+    "sphinx_copybutton",
+    "furo",
+    "markupsafe<2.1"
+]
+
+[tool.pylint.messages_control]
+disable = [
+    "too-many-nested-blocks",
+    "no-else-return",
+    "too-many-branches",
+    "too-many-statements",
+    "missing-function-docstring",
+    "consider-using-max-builtin",
+    "useless-object-inheritance",
+    "no-member",
+    "consider-using-enumerate",
+    "consider-using-f-string",
+    "invalid-name",
+    "missing-module-docstring",
+    "consider-using-dict-items",
+    "missing-class-docstring",
+    "deprecated-class",
+    "pointless-string-statement",
+    "too-many-locals",
+    "raise-missing-from",
+    "unnecessary-pass",
+]
+
+[tool.pylint.format]
+max-line-length = 120
+
+[tool.coverage.run]
+# Configuration of [coverage.py](https://coverage.readthedocs.io)
+# reporting which lines of your plugin are covered by tests
+source=["crossflow"]
+
+[tool.isort]
+# Configuration of [isort](https://isort.readthedocs.io)
+line_length = 120
+force_sort_within_sections = true
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 7d2b481..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-dask
-distributed
-fsspec
diff --git a/run_client_tests b/run_client_tests
deleted file mode 100755
index 5ce5977..0000000
--- a/run_client_tests
+++ /dev/null
@@ -1,112 +0,0 @@
-#!/usr/bin/env python
-from crossflow import filehandling, tasks, clients
-import tempfile
-from pathlib import Path
-
-
-def test_function_test(myclient, tmpdir):
-    def testit(f):
-        return f
-    fk = tasks.FunctionTask(testit)
-    fk.set_inputs(['f'])
-    fk.set_outputs(['x'])
-    p = tmpdir / "hello.txt"
-    p.write_text("content")
-    fh = filehandling.FileHandler()
-    pf = fh.load(p)
-    result = myclient.submit(fk, pf)
-    try:
-        assert isinstance(result.result(), filehandling.FileHandle)
-    except AssertionError:
-        print('Error: result.result() = {}'.format(result.result()))
-        raise
-
-
-def test_function_test_no_filehandler(myclient, tmpdir):
-    def testit(f):
-        return f
-    fk = tasks.FunctionTask(testit)
-    fk.set_inputs(['f'])
-    fk.set_outputs(['x'])
-    p = tmpdir / "hello.txt"
-    p.write_text("content")
-    result = myclient.submit(fk, p)
-    try:
-        assert isinstance(result.result(), filehandling.FileHandle)
-    except AssertionError:
-        print('Error: result.result() = {}'.format(result.result()))
-        raise
-
-
-def test_subprocess_test_data(myclient, tmpdir):
-    sk = tasks.SubprocessTask('cat file.txt')
-    sk.set_inputs(['file.txt'])
-    sk.set_outputs([tasks.STDOUT])
-    p = tmpdir / "hello.txt"
-    p.write_text("content")
-    fh = filehandling.FileHandler()
-    pf = fh.load(p)
-    ll = myclient.upload(pf)
-    result = myclient.submit(sk, ll)
-    try:
-        assert result.result() == 'content'
-    except AssertionError:
-        print('Error: result.result() = {}'.format(result.result()))
-
-
-def test_subprocess_test_no_filehandler(myclient, tmpdir):
-    sk = tasks.SubprocessTask('cat file.txt')
-    sk.set_inputs(['file.txt'])
-    sk.set_outputs([tasks.STDOUT])
-    p = tmpdir / "hello.txt"
-    p.write_text("content")
-    result = myclient.submit(sk, p)
-    try:
-        assert result.result() == 'content'
-    except AssertionError:
-        print('Error: result.result() = {}'.format(result.result()))
-
-
-def test_subprocess_test_file(myclient, tmpdir):
-    sk = tasks.SubprocessTask('cat file.txt')
-    sk.set_inputs(['file.txt'])
-    sk.set_outputs([tasks.STDOUT])
-    p = tmpdir / "hello.txt"
-    p.write_text("content")
-    fh = filehandling.FileHandler(tmpdir)
-    pf = fh.load(p)
-    ll = myclient.upload(pf)
-    result = myclient.submit(sk, ll)
-    try:
-        assert result.result() == 'content'
-    except AssertionError:
-        print('Error: result.result() = {}'.format(result.result()))
-
-
-def test_subprocess_test_s3(myclient, tmpdir):
-    sk = tasks.SubprocessTask('cat file.txt')
-    sk.set_inputs(['file.txt'])
-    sk.set_outputs([tasks.STDOUT])
-    p = tmpdir / "hello.txt"
-    p.write_text("content")
-    fh = filehandling.FileHandler('s3://bucket_name')
-    fp = fh.load(p)
-    ll = myclient.upload(fp)
-    result = myclient.submit(sk, ll)
-    try:
-        assert result.result() == 'content'
-    except AssertionError:
-        print('Error: result.result() = {}'.format(result.result()))
-
-
-if __name__ == '__main__':
-    myclient = clients.Client()
-    tmpdir = Path(tempfile.mkdtemp())
-    test_function_test(myclient, tmpdir)
-    test_function_test_no_filehandler(myclient, tmpdir)
-    test_subprocess_test_data(myclient, tmpdir)
-    test_subprocess_test_no_filehandler(myclient, tmpdir)
-    test_subprocess_test_file(myclient, tmpdir)
-    myclient.close()
-
-
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100755
index 08aedd7..0000000
--- a/setup.cfg
+++ /dev/null
@@ -1,2 +0,0 @@
-[metadata]
-description_file = README.md
diff --git a/setup.py b/setup.py
deleted file mode 100755
index 2eaa52e..0000000
--- a/setup.py
+++ /dev/null
@@ -1,120 +0,0 @@
-#!/usr/bin/env python
-"""  Setup script. Used by easy_install and pip. """
-
-import os
-import sys
-import re
-import textwrap
-
-from setuptools import setup, find_packages
-from setuptools import Extension as Ext
-
-
-"""Some functions for checking and showing errors and warnings."""
-
-
-def _print_admonition(kind, head, body):
-    tw = textwrap.TextWrapper(initial_indent='   ', subsequent_indent='   ')
-
-    print(".. {0}:: {1}".format(kind.upper(), head))
-    for line in tw.wrap(body):
-        print(line)
-
-
-def exit_with_error(head, body=''):
-    _print_admonition('error', head, body)
-    sys.exit(1)
-
-
-def print_warning(head, body=''):
-    _print_admonition('warning', head, body)
-
-
-def check_import(pkgname, pkgver):
-    """ Check for required Python packages. """
-    try:
-        mod = __import__(pkgname)
-        if mod.__version__ < pkgver:
-            raise ImportError
-    except ImportError:
-        exit_with_error(f"Can't find a local {pkgname} installation"
-                        f" with version >= {pkgver}. "
-                        f"Crossflow needs {pkgname} {pkgname} or greater"
-                        " to compile and run! "
-                        "Please see the ``README`` file.")
-
-    print(f"* Found {pkgname} {mod.__version__} package installed.")
-    globals()[pkgname] = mod
-
-
-def read(*rnames):
-    return open(os.path.join(os.path.dirname(__file__), *rnames)).read()
-
-
-"""Discover the package version"""
-VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
-VERSIONFILE = "crossflow/_version.py"
-verstrline = open(VERSIONFILE, "rt").read()
-mo = re.search(VSRE, verstrline, re.M)
-if mo:
-    verstr = mo.group(1)
-else:
-    raise RuntimeError(f"Cannot find version string in {VERSIONFILE}.")
-
-
-"""Check Python version"""
-print("* Checking Python version...")
-if sys.version_info[:2] < (3, 4):
-    exit_with_error("You need Python 3.4+ to install crossflow!")
-print("* Python version OK!")
-
-
-"""Set up crossflow."""
-
-
-class Extension(Ext, object):
-    pass
-
-
-setup_args = {
-    'name':             "crossflow",
-    'version':          verstr,
-    'description':      "A Python workflows system",
-    'long_description': read('README.md'),
-    'author':           "Charlie Laughton",
-    'author_email':     "charles.laughton@nottingham.ac.uk",
-    'url':              "",
-    'license':          "MIT license.",
-
-    'classifiers': [
-        'Development Status :: 3 - Alpha',
-        'Intended Audience :: Science/Research',
-        'Environment :: Console',
-        'License :: OSI Approved :: MIT License',
-        'Programming Language :: Python',
-        'Programming Language :: Python :: 3.4',
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-        'Topic :: Scientific/Engineering',
-        'Operating System :: MacOS :: MacOS X',
-        'Operating System :: POSIX',
-        'Operating System :: Unix'
-    ],
-
-    'packages': find_packages(),
-
-    'scripts': [
-               ],
-
-    'install_requires': [
-                'dask',
-                'distributed',
-                'fsspec',
-               ],
-
-    'zip_safe': False,
-}
-
-setup(**setup_args)
diff --git a/test/test_client.py b/test/test_client.py
deleted file mode 100644
index d78d73e..0000000
--- a/test/test_client.py
+++ /dev/null
@@ -1,9 +0,0 @@
-import os
-import subprocess
-
-
-def test_client():
-    SCRIPTLOC = os.path.dirname(os.path.dirname(__file__))
-    RUNSCRIPT = os.path.join(SCRIPTLOC, "run_client_tests")
-
-    subprocess.run(RUNSCRIPT, check=True)
diff --git a/tests/test_client.py b/tests/test_client.py
new file mode 100644
index 0000000..c82e339
--- /dev/null
+++ b/tests/test_client.py
@@ -0,0 +1,114 @@
+#!/usr/bin/env python
+from pathlib import Path
+
+import pytest
+
+from crossflow import clients, filehandling, tasks
+
+
+@pytest.fixture(scope="session")
+def myclient(request):
+    newclient = clients.Client()
+
+    def delete_client():
+        newclient.close()
+
+    request.addfinalizer(delete_client)
+    return newclient
+
+
+def test_function_test(myclient, tmpdir):
+    def testit(f):
+        return f
+
+    fk = tasks.FunctionTask(testit)
+    fk.set_inputs(["f"])
+    fk.set_outputs(["x"])
+    p = tmpdir / "hello.txt"
+    p.write_text("content", encoding="utf-8")
+    fh = filehandling.FileHandler()
+    pf = fh.load(p)
+    result = myclient.submit(fk, pf)
+    try:
+        assert isinstance(result.result(), filehandling.FileHandle)
+    except AssertionError:
+        print("Error: result.result() = {}".format(result.result()))
+        raise
+
+
+def test_function_test_no_filehandler(myclient, tmpdir):
+    def testit(f):
+        return f
+
+    fk = tasks.FunctionTask(testit)
+    fk.set_inputs(["f"])
+    fk.set_outputs(["x"])
+    p = tmpdir / "hello.txt"
+    p.write_text("content", encoding="utf-8")
+    result = myclient.submit(fk, p)
+    try:
+        assert isinstance(result.result(), filehandling.FileHandle)
+    except AssertionError:
+        print("Error: result.result() = {}".format(result.result()))
+        raise
+
+
+def test_subprocess_test_data(myclient, tmpdir):
+    sk = tasks.SubprocessTask("cat file.txt")
+    sk.set_inputs(["file.txt"])
+    sk.set_outputs([tasks.STDOUT])
+    p = tmpdir / "hello.txt"
+    p.write_text("content", encoding="utf-8")
+    fh = filehandling.FileHandler()
+    pf = fh.load(p)
+    ll = myclient.upload(pf)
+    result = myclient.submit(sk, ll)
+    try:
+        assert result.result() == "content"
+    except AssertionError:
+        print("Error: result.result() = {}".format(result.result()))
+
+
+def test_subprocess_test_no_filehandler(myclient, tmpdir):
+    sk = tasks.SubprocessTask("cat file.txt")
+    sk.set_inputs(["file.txt"])
+    sk.set_outputs([tasks.STDOUT])
+    p = tmpdir / "hello.txt"
+    p.write_text("content", encoding="utf-8")
+    result = myclient.submit(sk, p)
+    try:
+        assert result.result() == "content"
+    except AssertionError:
+        print("Error: result.result() = {}".format(result.result()))
+
+
+def test_subprocess_test_file(myclient, tmpdir):
+    sk = tasks.SubprocessTask("cat file.txt")
+    sk.set_inputs(["file.txt"])
+    sk.set_outputs([tasks.STDOUT])
+    p = tmpdir / "hello.txt"
+    p.write_text("content", encoding="utf-8")
+    fh = filehandling.FileHandler(tmpdir)
+    pf = fh.load(p)
+    ll = myclient.upload(pf)
+    result = myclient.submit(sk, ll)
+    try:
+        assert result.result() == "content"
+    except AssertionError:
+        print("Error: result.result() = {}".format(result.result()))
+
+
+# def test_subprocess_test_s3(myclient, tmpdir):
+#    sk = tasks.SubprocessTask('cat file.txt')
+#    sk.set_inputs(['file.txt'])
+#    sk.set_outputs([tasks.STDOUT])
+#    p = tmpdir / "hello.txt"
+#    p.write_text("content", encoding="utf-8")
+#    fh = filehandling.FileHandler('s3://bucket_name')
+#    fp = fh.load(p)
+#    ll = myclient.upload(fp)
+#    result = myclient.submit(sk, ll)
+#    try:
+#        assert result.result() == 'content'
+#    except AssertionError:
+#        print('Error: result.result() = {}'.format(result.result()))
diff --git a/test/test_filehandling.py b/tests/test_filehandling.py
similarity index 99%
rename from test/test_filehandling.py
rename to tests/test_filehandling.py
index 1e19f98..241b6cd 100644
--- a/test/test_filehandling.py
+++ b/tests/test_filehandling.py
@@ -1,6 +1,7 @@
-from crossflow import filehandling
 import os.path as op
 
+from crossflow import filehandling
+
 
 def test_data_protocol(tmpdir):
     d = tmpdir.mkdir("sub")
diff --git a/test/test_tasks.py b/tests/test_tasks.py
similarity index 95%
rename from test/test_tasks.py
rename to tests/test_tasks.py
index 4be41d2..e81d160 100644
--- a/test/test_tasks.py
+++ b/tests/test_tasks.py
@@ -1,6 +1,7 @@
-from crossflow import filehandling, tasks
 import pytest
 
+from crossflow import filehandling, tasks
+
 
 def test_subprocess_task_no_filehandles(tmpdir):
     sk = tasks.SubprocessTask("cat file.txt")
@@ -23,6 +24,7 @@ def test_subprocess_task_stdout(tmpdir):
     result = sk(pf)
     assert result == "content"
 
+
 def test_subprocess_task_constant_filehandle(tmpdir):
     sk = tasks.SubprocessTask("cat file.txt")
     sk.set_inputs(["file.txt"])
@@ -31,7 +33,7 @@ def test_subprocess_task_constant_filehandle(tmpdir):
     p.write("content")
     fh = filehandling.FileHandler()
     pf = fh.load(p)
-    sk.set_constant('file.txt', pf)
+    sk.set_constant("file.txt", pf)
     result = sk()
     assert result == "content"
 
@@ -64,6 +66,7 @@ def test_subprocess_task_globinputs_2(tmpdir):
     result.save(r)
     assert r.read() == "content\nmore content\n"
 
+
 def test_subprocess_task_globinputs_1(tmpdir):
     sk = tasks.SubprocessTask("cat *.txt > out.dat")
     sk.set_inputs(["*.txt"])
@@ -107,17 +110,19 @@ def test_subprocess_task_catch_fail():
     result = sk()
     assert isinstance(result, tasks.XflowError)
 
+
 def test_subprocesstask_with_constant():
     sk = tasks.SubprocessTask("head -{n} file.txt > out.dat")
     sk.set_inputs(["n", "file.txt"])
     sk.set_outputs(["out.dat"])
-    sk.set_constant('n', 1)
+    sk.set_constant("n", 1)
     fh = filehandling.FileHandler()
     pf = fh.create("tmp.txt")
-    pf.write_text('line 1\nline 2\nline 3')
+    pf.write_text("line 1\nline 2\nline 3")
     result = sk(pf)
-    assert result.read_text() == 'line 1\n'
-    
+    assert result.read_text() == "line 1\n"
+
+
 def test_function_task_basic():
     def mult(a, b):
         return a * b
@@ -147,6 +152,7 @@ def linecount(a):
     result = fk.run(pf)
     assert result == 3
 
+
 def test_function_task_with_output_filehandles(tmpdir):
     d = tmpdir.mkdir("sub")
     p = d.join("lines.txt")
@@ -157,9 +163,9 @@ def test_function_task_with_output_filehandles(tmpdir):
     def duplicate(a):
         with open(a) as f:
             data = f.read()
-        with open('out.dat', 'w') as f:
+        with open("out.dat", "w") as f:
             f.write(data)
-        return 'out.dat'
+        return "out.dat"
 
     fk = tasks.FunctionTask(duplicate)
     fk.set_inputs(["a"])
@@ -167,6 +173,7 @@ def duplicate(a):
     result = fk.run(pf)
     assert isinstance(result, filehandling.FileHandle)
 
+
 def test_function_task_with_constant_filehandles(tmpdir):
     d = tmpdir.mkdir("sub")
     p = d.join("lines.txt")
@@ -182,7 +189,7 @@ def linecount(a):
     fk = tasks.FunctionTask(linecount)
     fk.set_inputs(["a"])
     fk.set_outputs(["nlines"])
-    fk.set_constant('a', pf)
+    fk.set_constant("a", pf)
     result = fk.run()
     assert result == 3
 
@@ -202,7 +209,7 @@ def linecount(a):
     fk = tasks.FunctionTask(linecount)
     fk.set_inputs(["a"])
     fk.set_outputs(["nlines"])
-    result = fk.run({'a':pf})
+    result = fk.run({"a": pf})
     assert result == 3