236 support ubuntu 2404

.github/workflows/coverage.yml

@@ -2,37 +2,36 @@ name: Unit test and coverage
 on: [pull_request]
 jobs:
   coverage:
-    runs-on: ubuntu-16.04
+    runs-on: ubuntu-24.04
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v6
       with:
         submodules: recursive
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v6
       with:
-        python-version: 3.6
+        python-version: "3.10"
 
     - name: Install Sundials
       run: |
-        sudo apt-get install libsundials-serial-dev
+        sudo apt-get update
+        sudo apt-get install libsundials-dev
 
     - name: Install Python dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install -r requirements/setup.txt
+        python3 -m pip install --upgrade pip
 
     - name: Build and install
       run: |
-        python -m pip install -e .[test]
+        python3 -m pip install -e .[dev]
 
     - name: Unit & coverage tests
       run: |
-        python -m pytest --cov --cov-config=.coveragerc
+        FC_LONG_TESTS=1 python3 -m pytest -n auto --cov --cov-config=.coveragerc
 
     - name: Submit report to codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v5
       if: success()
-

.github/workflows/style.yml

@@ -2,25 +2,24 @@ name: Style
 on: [pull_request]
 jobs:
   style:
-    runs-on: ubuntu-16.04
+    runs-on: ubuntu-24.04
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v6
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v6
       with:
-        python-version: 3.6
+        python-version: "3.10"
 
     - name: Install tools
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install flake8
+        python3 -m pip install --upgrade pip
+        python3 -m pip install flake8
 
     - name: Check code style
       run: |
-        python --version
-        python -m flake8 --version
-        python -m flake8
-
+        python3 --version
+        python3 -m flake8 --version
+        python3 -m flake8

.gitignore

@@ -32,6 +32,7 @@ develop-eggs
 lib
 lib64
 venv*/
+.venv
 pyvenv*/
 
 # Installer logs

README.md

@@ -6,40 +6,45 @@
 
 This is a Python implementation of the Functional Curation (FC) language, intended for use with the Cardiac Electrophysiology Web Lab.
 
-Documentation on FC can be found [here](https://chaste.cs.ox.ac.uk/trac/wiki/FunctionalCuration), while the syntax of FC protocols is described [here](https://chaste.cs.ox.ac.uk/trac/wiki/FunctionalCuration/ProtocolSyntax).
+Documentation on FC can be found [here](https://chaste.github.io/docs/paper-tutorials/functionalcuration/), while the syntax of FC protocols is described [here](https://github.com/Chaste/trac_archive/wiki/Functional-Curation-_-Protocol-Syntax).
 
 An ongoing attempt to document the Web Lab and all its interconnected technologies can be viewed in the [weblab docs repository](https://github.com/ModellingWebLab/weblab_docs).
 
-## No Windows support
-
-**FC is tested/developed on Linux and OS/X. There are no plans to run it work on Windows**.
-
-It _might_ run on Windows, if you have installed CVODE with the shared libraries, and an MSVC compiler that matches your Python installation (see [here](https://wiki.python.org/moin/WindowsCompilers)).
-
-## Transition!
-
-This package is currently in transition, migrating the functional curation code from being a Chaste extension project to a standalone Python package.
-In particular, we're replacing the CellML and code-generation tool PyCml with [cellmlmanip](https://github.com/ModellingWebLab/cellmlmanip) to read and manipulate CellML code and a new module within `weblab-fc` to generate Model code.
-
-The code from before this transition started can be seen at the tag [`pycml-version`](https://github.com/ModellingWebLab/weblab-fc/tree/pycml-version), but crucial parts of PyCml weblab code are also temporarily stored in the [pycml](./pycml) directory.
-Most of the code from [pycml_protocol.py](./pycml/pycml_protocol.py) will have to be replaced by (1) changes to `fc` so that it extracts and stores _all_ the protocol information, and (2) a new code generation module in `fc` that can use information provides by weblab protocols to generate simulation code.
-(At the moment both `fc` and `pycml` read the protocol, but in the new code `fc` should gather all the information and then pass it to the code generation component of `fc`.)
+> [!NOTE]
+> ### No Windows support
+> 
+> FC is tested/developed on Linux and OS/X. There are no plans to make it run on Windows.
+> We recommend the [Windows Subsystem for Linux](https://github.com/microsoft/WSL).
+
+> [!WARNING]
+> ### Transition!
+> 
+> This package is currently in transition, migrating the functional curation code from 
+> being a Chaste extension project to a standalone Python package.
+> In particular, we're replacing the CellML and code-generation tool PyCml with 
+> [cellmlmanip](https://github.com/ModellingWebLab/cellmlmanip) to read and manipulate 
+> CellML code and a new module within `weblab-fc` to generate Model code.
+> 
+> The code from before this transition started can be seen at the tag 
+> [`pycml-version`](https://github.com/ModellingWebLab/weblab-fc/tree/pycml-version), 
+> but crucial parts of PyCml weblab code are also temporarily stored in the 
+> [pycml](./pycml) directory.
+> Most of the code from [pycml_protocol.py](./pycml/pycml_protocol.py) will have to be 
+> replaced by (1) changes to `fc` so that it extracts and stores _all_ the protocol 
+> information, and (2) a new code generation module in `fc` that can use information 
+> provides by weblab protocols to generate simulation code.
+> (At the moment both `fc` and `pycml` read the protocol, but in the new code `fc` 
+> should gather all the information and then pass it to the code generation component of `fc`.)
 
 ## Installation
 
-In order to build the package you need Cython and numpy. These can be installed with:
-```sh
-pip install -r requirements/setup.txt
-```
-
 The ontologies used are in a separate module, to install this run
 
 ```sh
-git submodule init
-git submodule update
+git submodule update --init
 ```
 
-You also need to have CVODE (from Sundials) installed. If you do this with your system package
+You also need to have CVODE (from Sundials v3+) installed. If you do this with your system package
 manager no further setup is (probably) needed. Alternatively you can install it using `conda`:
 ```sh
 conda install sundials -c conda-forge
@@ -52,25 +57,11 @@ export LDFLAGS="-L$HOME/anaconda3/envs/weblab/lib"
 ```
 
 Because the `weblab_fc` module has Cython components, it needs to be compiled before you can use it.
-Compilation is performed using Python's [`distutils`](https://docs.python.org/3/library/distutils.html) and [`setuptools`](https://setuptools.readthedocs.io/en/latest/), and happens automatically when you install the package using `setup.py`.
+Compilation is performed using Python's [`setuptools`](https://setuptools.readthedocs.io/en/latest/), and happens automatically when you install the package.
 For developers, this can be done using:
 
 ```sh
-pip install -e .[dev,test]
+python3 -m pip install -e ."[dev]"
 ```
 
 Note that you'll need to repeat this step after any changes to Cython files (e.g. `.pyx` or `.pxd` files), because these don't automatically get recompiled.
-
-## Full installation steps on Jonathan's Macbook (slightly out of date)
-
-```sh
-export CONDA_ENV=weblab-fc-py36
-conda create -n $CONDA_ENV python=3.6
-conda activate $CONDA_ENV
-conda install -c conda-forge sundials=4 pytables scipy numpy numexpr
-pip install -r requirements/setup.txt
-./requirements/weblab_cg.sh
-export CFLAGS="-I/anaconda3/envs/$CONDA_ENV/include"
-export LDFLAGS="-L/anaconda3/envs/$CONDA_ENV/lib"
-pip install -e .[dev,test]
-```

fc/__init__.py

@@ -15,8 +15,9 @@
 finally:
     # Always manually delete frame
     # https://docs.python.org/2/library/inspect.html#the-interpreter-stack
-    del(frame)
-del(os, inspect)
+    del frame
+del os
+del inspect
 
 
 from .protocol import Protocol  # noqa:F401,E402

fc/environment.py

@@ -20,7 +20,7 @@ class Environment(object):
     Variables not found within the environment are looked up in its "default delegatee".
 
     For more information, see
-    https://chaste.cs.ox.ac.uk/trac/wiki/FunctionalCuration/ProtocolSyntax#Identifiersandnameresolution
+    https://github.com/Chaste/trac_archive/wiki/Functional-Curation-_-Protocol-Syntax#Identifiersandnameresolution
     """
     next_ident = [0]
 
@@ -57,14 +57,14 @@ def define_names(self, names, values):
     def evaluate_expr(self, expr_str, env):
         from fc.parsing.CompactSyntaxParser import CompactSyntaxParser as csp
 
-        parse_action = csp.expr.parseString(expr_str, parseAll=True)
+        parse_action = csp.expr.parse_string(expr_str, parse_all=True)
         expr = parse_action[0].expr()
         return expr.evaluate(env)
 
     def evaluate_statement(self, stmt_str, env):
         from fc.parsing.CompactSyntaxParser import CompactSyntaxParser as csp
 
-        parse_action = csp.stmt_list.parseString(stmt_str, parseAll=True)
+        parse_action = csp.stmt_list.parse_string(stmt_str, parse_all=True)
         stmt_list = parse_action[0].expr()
         return env.execute_statements(stmt_list)
 
@@ -78,14 +78,14 @@ def look_up(self, name):
 #         try:
 #             return self.bindings[name]
 #         except KeyError:
-#             print 'Key error looking up', name, 'in', self
+#             print('Key error looking up', name, 'in', self)
 #             import sys
 #             tb = sys.exc_info()[2]
 #             while tb:
 #                 local_vars = tb.tb_frame.f_locals
 #                 obj = local_vars.get('self', None)
 #                 if obj and isinstance(obj, DelegatingDict):
-#                     print 'Looked for', local_vars['key'], 'in', obj._env
+#                     print('Looked for', local_vars['key'], 'in', obj._env)
 #                 tb = tb.tb_next
 #             self.debug_delegatees('root')
 #             raise
@@ -101,7 +101,7 @@ def set_delegatee_env(self, delegatee, prefix=""):
                 "The name prefix '" + prefix +
                 "' has already been used in this context. Check your simulations, imports, etc.")
         self.delegatees[prefix] = delegatee
-#         print 'Delegating to', delegatee, 'for', prefix, 'in', self
+#         print('Delegating to', delegatee, 'for', prefix, 'in', self)
         self.bindings.set_delegatee(delegatee.bindings, prefix)
         self.unwrapped_bindings.set_delegatee(delegatee.unwrapped_bindings, prefix)
 

fc/language/expressions/abstract.py

@@ -129,13 +129,13 @@ def get_defining_environments(self, env):
             return self._defining_envs
         except AttributeError:
             self._root_defining_env = env  # For paranoia checking that the cache is valid
-            d = self._defining_envs = {}
-            l = self._used_var_local_names = []  # noqa: E741
+            defining_envs = self._defining_envs = {}
+            used_local_names = self._used_var_local_names = []  # noqa: E741
             for name in self.used_variable_list:
                 local_name = name[name.rfind(':') + 1:]
-                l.append(local_name)
-                d[local_name] = env.find_defining_environment(name)
-            return d
+                used_local_names.append(local_name)
+                defining_envs[local_name] = env.find_defining_environment(name)
+            return defining_envs
 
     @property
     def compiled_function(self):
@@ -154,9 +154,9 @@ def used_variable_list(self):
         try:
             return self._used_var_list
         except AttributeError:
-            l = self._used_var_list = list(self.used_variables)  # noqa: E741
-            l.sort()
-            return l
+            used_var_list = self._used_var_list = list(self.used_variables)  # noqa: E741
+            used_var_list.sort()
+            return used_var_list
 
     @property
     def used_variables(self):