add a pre-commit file and configuration

.github/workflows/pythonpackage.yml

@@ -70,7 +70,7 @@ jobs:
         CIBW_BEFORE_ALL_LINUX: >
             mkdir /boost &&
             pushd /boost &&
-            curl -L -o boost_1_76_0.tar.bz2 'https://sourceforge.net/projects/boost/files/boost/1.76.0/boost_1_76_0.tar.bz2' && 
+            curl -L -o boost_1_76_0.tar.bz2 'https://sourceforge.net/projects/boost/files/boost/1.76.0/boost_1_76_0.tar.bz2' &&
             tar xf boost_1_76_0.tar.bz2 &&
             popd
         CIBW_ENVIRONMENT_LINUX: "${{ matrix.arch == 'aarch64' && 'BOOST_ROOT=/boost/boost_1_76_0 CMAKE_ARGS=-DCMAKE_POLICY_VERSION_MINIMUM=3.5' || 'BOOST_ROOT=/boost/boost_1_76_0' }}"
@@ -86,7 +86,7 @@ jobs:
     - uses: actions/checkout@v7
       with:
         fetch-depth: 0  # for setuptools_scm to find tags
-    
+
     - name: Install boost
       run:
         mkdir /tmp/boost &&

.github/workflows/update-helics.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v7
-    
+
     - name: Set git config for commits
       run: |
         git config --global user.name "github-actions[bot]"

.pre-commit-config.yaml

@@ -0,0 +1,74 @@
+exclude: ^(helics-src/|helics-src\.downloaded/)
+
+ci:
+  autoupdate_branch: "main"
+
+repos:
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.5.1
+    hooks:
+      - id: black
+        args:
+          [
+            "--line-length=100",
+            "--target-version=py311",
+            "--target-version=py312",
+            "--target-version=py313",
+            "--target-version=py314",
+          ]
+
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.20.0
+    hooks:
+      - id: blacken-docs
+        args:
+          [
+            "--line-length=100",
+            "--target-version=py311",
+            "--target-version=py312",
+            "--target-version=py313",
+            "--target-version=py314",
+          ]
+        additional_dependencies: [black==26.5.1]
+
+  - repo: https://github.com/Lucas-C/pre-commit-hooks
+    rev: v1.5.6
+    hooks:
+      - id: remove-tabs
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-shebang-scripts-are-executable
+      - id: check-symlinks
+      - id: check-toml
+      - id: check-yaml
+        args: ["--allow-multiple-documents"]
+      - id: debug-statements
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.25
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  - repo: https://github.com/mgedmin/check-manifest
+    rev: "0.51"
+    hooks:
+      - id: check-manifest
+        stages: [manual]
+        args: ["--no-build-isolation"]
+        additional_dependencies:
+          - build
+          - ninja
+          - scikit-build-core
+          - setuptools-scm

README.md

@@ -27,6 +27,7 @@ To use the project:
 
 ```python
 import helics as h
+
 h.helicsGetVersion()
 ```
 
@@ -54,4 +55,4 @@ $ python -c "import helics as h; import json; print(json.dumps(h.helicsGetSystem
 ```
 # Citation
 General citation for HELICS:
-T. Hardy, B. Palmintier, P. Top, D. Krishnamurthy and J. Fuller, "HELICS: A Co-Simulation Framework for Scalable Multi-Domain Modeling and Analysis," in IEEE Access, doi: 10.1109/ACCESS.2024.3363615, available at [https://ieeexplore.ieee.org/document/10424422](https://ieeexplore.ieee.org/document/10424422/)
+T. Hardy, B. Palmintier, P. Top, D. Krishnamurthy and J. Fuller, "HELICS: A Co-Simulation Framework for Scalable Multi-Domain Modeling and Analysis," in IEEE Access, doi: 10.1109/ACCESS.2024.3363615, available at [https://ieeexplore.ieee.org/document/10424422](https://ieeexplore.ieee.org/document/10424422/)

docs/callbacks.md

@@ -3,14 +3,14 @@
 There are several HELICS functionalities that allow for the definition of custom behavior through the use of custom callback functions. Two specific examples are the definition of the filter behavior when implementing a filter federate and the other is the response to a custom query. In both cases custom code needs to be written to define behavior when HELICS needs to perform a specific action (filter a message, respond to a query). There are a few steps to implement callbacks in PyHELICS
 
 ## Define User Data
-The callback function generally exists outside the scope of other code and thus, if the functionality defined in the callback needs data from, say, the federate, that data has to be carried into the callback through a custom class generically called "user data". This user data is defined as a class that is instantiated and filled as a part of federate operation.  
+The callback function generally exists outside the scope of other code and thus, if the functionality defined in the callback needs data from, say, the federate, that data has to be carried into the callback through a custom class generically called "user data". This user data is defined as a class that is instantiated and filled as a part of federate operation.
 
 ```python
-# Store what ever data you'd like. 
-# A reference to this object is passed to the filter callback. 
+# Store what ever data you'd like.
+# A reference to this object is passed to the filter callback.
 # You don't need to use this if you don't want to.
 class UserData:
-    def __init__(self, iteration_count = None):
+    def __init__(self, iteration_count=None):
         self.pi = 3.14
         self.e = 2.718
         self.interation_count = iteration_count
@@ -24,19 +24,23 @@ This is where the real C-to-Python magic happens, using the "cffi" library. As t
 @h.ffi.callback("void logger(HelicsMessage, void* userData)")
 def filter_callback(mess, userData):
     # Filter operation code here
+    pass
+
 
 # Query callback
-@h.ffi.callback("void query(const char *query, int querySize, HelicsQueryBuffer buffer, void *user_data)")
-def query_callback(query_ptr, size:int, query_buffer_ptr, user_data):
-    query_str = h.ffi.string(query_ptr,size).decode()
+@h.ffi.callback(
+    "void query(const char *query, int querySize, HelicsQueryBuffer buffer, void *user_data)"
+)
+def query_callback(query_ptr, size: int, query_buffer_ptr, user_data):
+    query_str = h.ffi.string(query_ptr, size).decode()
     query_buffer = h.HelicsQueryBuffer(query_buffer_ptr)
     # Query operation code here
-
+    pass
 ```
 
 In the case of the query callback, you can see there are two other bits that need to be added in.
-  
-  1 - The query string is passed in as a C pointer. If you've only worked in Python, you might wonder what a "pointer" is. So does Python; the "cffi" library is used to translate the data the pointer is referencing into something Python recognizes as a string. 
+
+  1 - The query string is passed in as a C pointer. If you've only worked in Python, you might wonder what a "pointer" is. So does Python; the "cffi" library is used to translate the data the pointer is referencing into something Python recognizes as a string.
   2 - The query response that will be created by the callback function must be put into a pre-constructed databuffer that is passed in when the callback is made ("HelicsQueryBuffer buffer" in the above C signature). HELICS will read this buffer to get the response of the callback. Again, pointers are involved so we use the "cffi" library to make them something Python can deal with.
 
 ## Register the Callback
@@ -49,7 +53,7 @@ Last step, with the callback defined we need to "register" it so that HELICS kno
 def main():
     ...
     f1 = h.helicsFederateRegisterFilter(fFed, h.HELICS_FILTER_TYPE_CUSTOM, "filter1")
-    userdata = UserData(iteration_count = 10)
+    userdata = UserData(iteration_count=10)
     user_data_handle = h.ffi.new_handle(userdata)
     h.helicsFilterSetCustomCallback(f1, filter_callback, user_data_handle)
 
@@ -58,10 +62,9 @@ def main():
 def main():
     ...
     fed = h.helicsCreateValueFederateFromConfig("math_fed.json")
-    user_data = UserData(iteration_count = 10)
+    user_data = UserData(iteration_count=10)
     user_data_handle = h.ffi.new_handle(user_data)
     h.helicsFederateSetQueryCallback(fed, query_callback, user_data_handle)
-
 ```
 
 In both cases, the user data is defined, a "handle" to the user data is created, and the callback functions are registered using specific HELICS APIs.
@@ -72,44 +75,49 @@ Here are the full code for completeness sake. As of this writing, there is not a
 
 ### Filter Federate Code
 ``` python
-
 class UserData:
-    def __init__(self, iteration_count = None):
+    def __init__(self, iteration_count=None):
         self.pi = 3.14
         self.e = 2.718
         self.interation_count = iteration_count
-
+
+
 @h.ffi.callback("void logger(HelicsMessage, void* userData)")
 def filter_callback(mess, userData):
     # Filter operation code here
-
+    pass
+
 
 def main():
     fed = h.helicsCreateValueFederateFromConfig("math_fed.json")
     f1 = h.helicsFederateRegisterFilter(fed, h.HELICS_FILTER_TYPE_CUSTOM, "filter1")
-    userdata = UserData(iteration_count = 10)
+    userdata = UserData(iteration_count=10)
     user_data_handle = h.ffi.new_handle(userdata)
     h.helicsFilterSetCustomCallback(f1, filter_callback, user_data_handle)
 ```
 
 ### Query Response Code
 ```Python
 class UserData:
-    def __init__(self, iteration_count = None):
+    def __init__(self, iteration_count=None):
         self.pi = 3.14
         self.e = 2.718
         self.interation_count = iteration_count
 
-@h.ffi.callback("void query(const char *query, int querySize, HelicsQueryBuffer buffer, void *user_data)")
-def query_callback(query_ptr, size:int, query_buffer_ptr, user_data):
-    query_str = h.ffi.string(query_ptr,size).decode()
+
+@h.ffi.callback(
+    "void query(const char *query, int querySize, HelicsQueryBuffer buffer, void *user_data)"
+)
+def query_callback(query_ptr, size: int, query_buffer_ptr, user_data):
+    query_str = h.ffi.string(query_ptr, size).decode()
     query_buffer = h.HelicsQueryBuffer(query_buffer_ptr)
     # Query operation code here
-
+    pass
+
 
 def main():
     fed = h.helicsCreateValueFederateFromConfig("math_fed.json")
-    user_data = UserData(iteration_count = 10)
+    user_data = UserData(iteration_count=10)
     user_data_handle = h.ffi.new_handle(user_data)
     h.helicsFederateSetQueryCallback(fed, query_callback, user_data_handle)
 

docs/examples/10-federates-1-topic/pisender.py

@@ -38,7 +38,9 @@ def main(n):
         fed.request_next_step()
 
         fed.publications[f"globaltopic"].publish(value)
-        print(f"{federate_name}: Sending value pi = {value} at time {fed.current_time} on globaltopic")
+        print(
+            f"{federate_name}: Sending value pi = {value} at time {fed.current_time} on globaltopic"
+        )
 
         # Computing user needs
         time.sleep(float(n) * (1 + (0.5 - random.random()) / 10))

docs/examples/website_pythonic_interface/pythonic_interface.py

@@ -47,19 +47,25 @@
 # Read data as bytes
 mFed.publications["TestFederate/publication"].publish(b"bytes")
 assert mFed.request_time(2.0) == 1.0
-print(f'mFed.subscriptions["TestFederate/publication"].bytes: {mFed.subscriptions["TestFederate/publication"].bytes}')
+print(
+    f'mFed.subscriptions["TestFederate/publication"].bytes: {mFed.subscriptions["TestFederate/publication"].bytes}'
+)
 assert mFed.subscriptions["TestFederate/publication"].bytes == b"bytes"
 
 # Read data as a string
 mFed.publications["TestFederate/publication"].publish("string")
 mFed.request_time(3.0)
-print(f'mFed.subscriptions["TestFederate/publication"].string: {mFed.subscriptions["TestFederate/publication"].string}')
+print(
+    f'mFed.subscriptions["TestFederate/publication"].string: {mFed.subscriptions["TestFederate/publication"].string}'
+)
 assert mFed.subscriptions["TestFederate/publication"].string == "string"
 
 # Read data as a value and let HELICS figure out the right data type
 mFed.publications["TestFederate/publication"].publish("value")
 mFed.request_time(4.0)
-print(f'mFed.subscriptions["TestFederate/publication"].value: {mFed.subscriptions["TestFederate/publication"].value}')
+print(
+    f'mFed.subscriptions["TestFederate/publication"].value: {mFed.subscriptions["TestFederate/publication"].value}'
+)
 assert mFed.subscriptions["TestFederate/publication"].value == "value"
 
-print("Example complete")
+print("Example complete")

docs/examples/website_usage/broker.py

@@ -9,4 +9,4 @@
 broker = h.helicsCreateBroker("zmq", "", "-f 2 --loglevel=trace")
 
 while h.helicsBrokerIsConnected(broker):
-    time.sleep(1)
+    time.sleep(1)

docs/examples/website_usage/federate_1.py

@@ -32,4 +32,4 @@
     time.sleep(1)
 
 h.helicsFederateDisconnect(vfed)
-h.helicsFederateDestroy(vfed)
+h.helicsFederateDestroy(vfed)

docs/examples/website_usage/federate_2.py

@@ -28,4 +28,4 @@
     print("RECEIVER: Received value = {} at time {} from SENDER".format(value, currenttime))
 
 h.helicsFederateDisconnect(vfed)
-h.helicsFederateDestroy(vfed)
+h.helicsFederateDestroy(vfed)

docs/pythonic-interface.md

@@ -53,20 +53,26 @@ print("Publishing string and reading as various data types")
 # Read data as bytes
 mFed.publications["TestFederate/publication"].publish(b"bytes")
 assert mFed.request_time(2.0) == 1.0
-print(f'mFed.subscriptions["TestFederate/publication"].bytes: {mFed.subscriptions["TestFederate/publication"].bytes}')
+print(
+    f'mFed.subscriptions["TestFederate/publication"].bytes: {mFed.subscriptions["TestFederate/publication"].bytes}'
+)
 assert mFed.subscriptions["TestFederate/publication"].bytes == b"bytes"
 
 # Read data as a string
 mFed.publications["TestFederate/publication"].publish("string")
 mFed.request_time(3.0)
-print(f'mFed.subscriptions["TestFederate/publication"].string: {mFed.subscriptions["TestFederate/publication"].string}')
+print(
+    f'mFed.subscriptions["TestFederate/publication"].string: {mFed.subscriptions["TestFederate/publication"].string}'
+)
 assert mFed.subscriptions["TestFederate/publication"].string == "string"
 
 # Read data as a value and let HELICS figure out the right data type
 mFed.publications["TestFederate/publication"].publish("value")
 mFed.request_time(4.0)
-print(f'mFed.subscriptions["TestFederate/publication"].value: {mFed.subscriptions["TestFederate/publication"].value}')
+print(
+    f'mFed.subscriptions["TestFederate/publication"].value: {mFed.subscriptions["TestFederate/publication"].value}'
+)
 assert mFed.subscriptions["TestFederate/publication"].value == "value"
 
 print("Example complete")
-```
+```

helics/_build.py

@@ -21,7 +21,11 @@
 )
 PYHELICS_INSTALL = os.getenv("PYHELICS_INSTALL", HELICS_INSTALL)
 if not os.path.isdir(PYHELICS_INSTALL):
-    warnings.warn("PYHELICS_INSTALL ({}) is not a directory. Using DEFAULT_INSTALL ({})".format(PYHELICS_INSTALL, CURRENT_INSTALL))
+    warnings.warn(
+        "PYHELICS_INSTALL ({}) is not a directory. Using DEFAULT_INSTALL ({})".format(
+            PYHELICS_INSTALL, CURRENT_INSTALL
+        )
+    )
     PYHELICS_INSTALL = CURRENT_INSTALL
 
 files = [
@@ -76,7 +80,11 @@ def _load_library():
         for file in os.listdir(os.path.join(PYHELICS_INSTALL, "bin")):
             if "helics" in file and file.endswith(".dll"):
                 try:
-                    logger.debug("dlopen helics library in {}".format(os.path.join(PYHELICS_INSTALL, "bin", file)))
+                    logger.debug(
+                        "dlopen helics library in {}".format(
+                            os.path.join(PYHELICS_INSTALL, "bin", file)
+                        )
+                    )
                     lib = ffi.dlopen(os.path.join(PYHELICS_INSTALL, "bin", file))
                     break
                 except OSError as _:
@@ -112,7 +120,9 @@ def _load_library():
         else:
             for file in reversed(sorted(os.listdir(lib_folder), key=len)):
                 if "helicsSharedLibd." in file or "libhelicsd." in file and file.endswith(".dylib"):
-                    logger.debug("dlopen debug helics library in {}".format(os.path.join(lib_folder, file)))
+                    logger.debug(
+                        "dlopen debug helics library in {}".format(os.path.join(lib_folder, file))
+                    )
                     lib = ffi.dlopen(os.path.join(lib_folder, file))
                     break
             else:
@@ -141,7 +151,11 @@ def _load_library():
             for file in reversed(sorted(os.listdir(lib_folder), key=len)):
                 if "helicsSharedLibd." in file or "libhelicsd." in file and file.endswith(".so"):
                     try:
-                        logger.debug("dlopen debug helics library in {}".format(os.path.join(lib_folder, file)))
+                        logger.debug(
+                            "dlopen debug helics library in {}".format(
+                                os.path.join(lib_folder, file)
+                            )
+                        )
                         lib = ffi.dlopen(os.path.join(lib_folder, file))
                         break
                     except: