Change CI to use micromamba and nox

.github/workflows/ci.yml

@@ -44,16 +44,14 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Spell check
-        run: |
-          pip install codespell
-          codespell --config .github/linters/.codespellrc
-          
+      - name: Install nox
+        run: pip install nox
+
       - name: Code format
-        run: |
-          pip install flake8
-          flake8 --config .github/linters/.flake8 src
-          flake8 --config .github/linters/.flake8 tests
+        run: nox -s linter
+
+      - name: Spell check
+        run: nox -s codespell          
 
   test:
     name: (Test ${{ matrix.python-version }}, ${{ matrix.os }})
@@ -74,32 +72,25 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup conda/python
-        uses: conda-incubator/setup-miniconda@v3
+        uses: mamba-org/setup-micromamba@v2
         with:  # ci_environment.yml specifies sundials version to compile
-          auto-update-conda: true
-          miniconda-version: latest
           environment-file: environments/ci_environment.yml
-          python-version: ${{ matrix.python-version }}
-          activate-environment: sun
-          channels: conda-forge
-          conda-remove-defaults: "true"
+          create-args: python=${{ matrix.python-version }}
 
       - name: Verify environment
         run: |
-          conda info
-          conda list
+          micromamba info
+          micromamba list
 
       - name: Install scikit-sundae
         run: |
           python -m pip install --upgrade pip
-          pip install .
+          pip install .[tests]
 
       - name: List info
         run: |
-          conda info
-          conda list
+          micromamba info
+          micromamba list
                 
       - name: Pytest
-        run: |
-          pip install pandas pytest
-          pytest .
+        run: nox -s tests -- no-reports

inprogress/getfullargspec.py

@@ -0,0 +1,97 @@
+import inspect
+from collections import namedtuple
+from inspect import (_POSITIONAL_ONLY, _POSITIONAL_OR_KEYWORD, _VAR_POSITIONAL,
+                     _KEYWORD_ONLY, _VAR_KEYWORD,)
+
+from jax import jit as jjit
+from numba import jit as njit
+
+
+def py_func(a: int, b: int, *c, x: int = 1, y: int = 2, **z):
+    return x + y
+
+
+@njit
+def nb_func(a: int, b: int, *c, x: int = 1, y: int = 2, **z):
+    return x + y
+
+
+@jjit
+def jax_func(a: int, b: int, *c, x: int = 1, y: int = 2, **z):
+    return x + y
+
+
+class py_call:
+
+    def __call__(self, a: int, b: int, *c, x: int = 1, y: int = 2, **z):
+        return x + y
+
+    @classmethod
+    def call(cls, a: int, b: int, *c, x: int = 1, y: int = 2, **z):
+        return x + y
+
+
+FullArgSpec = namedtuple(
+    'FullArgSpec',
+    'args, varargs, varkw, defaults, kwonlyargs, kwonlydefaults, annotations',
+)
+
+
+def getfullargspec(func) -> FullArgSpec:
+
+    try:
+        sig = inspect.signature(func)
+    except Exception as ex:
+        raise TypeError('unsupported callable') from ex
+
+    args = []
+    varargs = None
+    varkw = None
+    posonlyargs = []
+    kwonlyargs = []
+    annotations = {}
+    defaults = ()
+    kwdefaults = {}
+
+    if sig.return_annotation is not sig.empty:
+        annotations['return'] = sig.return_annotation
+
+    for param in sig.parameters.values():
+        kind = param.kind
+        name = param.name
+
+        if kind is _POSITIONAL_ONLY:
+            posonlyargs.append(name)
+            if param.default is not param.empty:
+                defaults += (param.default,)
+        elif kind is _POSITIONAL_OR_KEYWORD:
+            args.append(name)
+            if param.default is not param.empty:
+                defaults += (param.default,)
+        elif kind is _VAR_POSITIONAL:
+            varargs = name
+        elif kind is _KEYWORD_ONLY:
+            kwonlyargs.append(name)
+            if param.default is not param.empty:
+                kwdefaults[name] = param.default
+        elif kind is _VAR_KEYWORD:
+            varkw = name
+
+        if param.annotation is not param.empty:
+            annotations[name] = param.annotation
+
+    if not kwdefaults:
+        kwdefaults = None
+
+    if not defaults:
+        defaults = None
+
+    return FullArgSpec(posonlyargs + args, varargs, varkw, defaults,
+                       kwonlyargs, kwdefaults, annotations)
+
+
+print('py:', getfullargspec(py_func))
+print('nb:', getfullargspec(nb_func))
+print('jax:', getfullargspec(jax_func))
+print('call:', getfullargspec(py_call()))
+print('cls:', getfullargspec(py_call.call))

noxfile.py

@@ -5,6 +5,8 @@
 
 import nox
 
+nox.options.sessions = []
+
 
 @nox.session(name='cleanup', python=False)
 def run_cleanup(_):
@@ -27,6 +29,8 @@ def run_flake8(session):
     Use the optional 'format' argument to run autopep8 prior to the linter.
 
     """
+
+    session.run('pip', 'install', '--upgrade', 'flake8')
 
     if 'format' in session.posargs:
         session.run('autopep8', '.', '--in-place', '--recursive',
@@ -44,9 +48,10 @@ def run_codespell(session):
     the files. Otherwise, you will only see a summary of the found errors.
 
     """
+
+    session.run('pip', 'install', '--upgrade', 'codespell')
 
     command = ['codespell', '--config=.github/linters/.codespellrc']
-
     if 'write' in session.posargs:
         command.insert(1, '-w')
 
@@ -84,14 +89,21 @@ def run_pytest(session):
 
     """
 
-    command = [
-        'pytest',
-        '--cov=src/sksundae',
-        '--cov-report=html:reports/htmlcov',
-        '--cov-report=xml:reports/coverage.xml',
-        '--junitxml=reports/junit.xml',
-        'tests/',
-    ]
+    if 'no-reports' in session.posargs:
+        command = [
+            'pytest',
+            '--cov=src/sksundae',
+            'tests/',
+        ]
+    else:
+        command = [
+            'pytest',
+            '--cov=src/sksundae',
+            '--cov-report=html:reports/htmlcov',
+            '--cov-report=xml:reports/coverage.xml',
+            '--junitxml=reports/junit.xml',
+            'tests/',
+        ]
 
     for arg in session.posargs:
         if arg.startswith('parallel='):

pyproject.toml

@@ -51,35 +51,29 @@ version = {attr = "sksundae.__version__"}
 where = ["src"]
 
 [project.optional-dependencies]
-dev = [
-    "nox",
-    "pandas",
-    "pytest",
-    "pytest-cov",
-    "pytest-xdist",
-    "genbadge[all]",
-    "flake8",
-    "autopep8",
-    "codespell",
-    "sphinx",
-    "myst-nb",
-    "sphinx-design",
-    "sphinx-autoapi",
-    "sphinx-favicon",
-    "sphinx-copybutton",
-    "pydata-sphinx-theme",
-    "matplotlib",
-]
 docs = [
     "sphinx",
     "myst-nb",
     "sphinx-design",
     "sphinx-autoapi",
-    "sphinx-favicon",
     "sphinx-copybutton",
     "pydata-sphinx-theme",
     "matplotlib",
 ]
+tests = [
+    "pandas",
+    "pytest",
+    "pytest-cov",
+    "pytest-xdist",
+]
+dev = [
+    "nox",
+    "flake8",
+    "autopep8",
+    "codespell",
+    "genbadge[all]",
+    "scikit-sundae[docs,tests]",
+]
 
 [project.urls]
 Homepage = "https://github.com/NREL/scikit-sundae"