Sync environment.yml with pyproject.toml via pyproject2conda pre-commit hook (#713)

* Sync environment.yml with pyproject.toml via pyproject2conda pre-commit hook

- Add pyproject2conda pre-commit hook to regenerate environment.yml from
  pyproject.toml when deps change (base + dev extra + conda-only deps)
- Add [tool.pyproject2conda] with conda-forge channel in pyproject.toml
- Regenerate environment.yml; adds pymc-marketing and full dev deps

Closes #712

Co-authored-by: Cursor <cursoragent@cursor.com>

* Address adversarial review: CI env-sync check, CONTRIBUTING note, hook comments

- Add check-environment-yml CI job to fail if environment.yml is out of sync
- Document in CONTRIBUTING that environment.yml is generated from pyproject.toml
- Comment in pre-commit-config: python>=3.12 and conda-only deps

Co-authored-by: Cursor <cursoragent@cursor.com>

* ci: set persist-credentials: false in check-environment-yml job

Address GitHub Advanced Security warning about credential persistence.

Co-authored-by: Cursor <cursoragent@cursor.com>

* Move pymc-marketing to docs extra; document pip vs conda

- pyproject.toml: remove pymc-marketing from core deps, add to docs extra
- environment.yml: regenerated (no pymc-marketing in default env)
- Integration tests: skip BSTS tests when pymc_marketing not installed (importorskip)
- AGENTS.md: deps in pyproject.toml; supported dev setup is conda (pip -e .[dev] lacks conda-only tooling)
- README: add fallback line for PyMC install issues (try conda)
- ci.yml: add security comment for test job persist-credentials

Co-authored-by: Cursor <cursoragent@cursor.com>

* Skip BSTS coverage tests when pymc-marketing not installed

Add autouse fixture to TestBayesianBasisExpansionTimeSeriesCoverage that
calls pytest.importorskip('pymc_marketing') so the whole class is skipped
when the optional dependency is missing (e.g. in CI without docs extra).

Co-authored-by: Cursor <cursoragent@cursor.com>
Made-with: Cursor

---------

Co-authored-by: Cursor <cursoragent@cursor.com>

Author: drbenvincent

.github/workflows/ci.yml

@@ -9,6 +9,33 @@ on:
 permissions: {}
 
 jobs:
+  check-environment-yml:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          # Security: do not set to true — prevents credential leakage (GitHub Advanced Security).
+          persist-credentials: false
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        with:
+          python-version: "3.12"
+      - name: Install pyproject2conda
+        run: pip install pyproject2conda
+      - name: Regenerate environment.yml (same args as pre-commit hook)
+        run: |
+          pyproject2conda yaml -e dev -o /tmp/environment.generated.yml -n CausalPy \
+            -w force --no-header \
+            --python-include "python>=3.12" \
+            -d make -d pip -d pymc-bart -r "marimo[mcp]"
+      - name: Check environment.yml is in sync with pyproject.toml
+        run: |
+          # Compare YAML body only (skip 9-line autogenerated header in environment.yml)
+          tail -n +10 environment.yml > /tmp/environment.current.yml
+          diff -u /tmp/environment.current.yml /tmp/environment.generated.yml && echo "environment.yml is in sync with pyproject.toml"
+
   test:
     runs-on: ubuntu-latest
     permissions:
@@ -20,6 +47,7 @@ jobs:
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
+          # Security: do not set to true — prevents credential leakage (GitHub Advanced Security).
           persist-credentials: false
       - name: Set up Python
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0

.pre-commit-config.yaml

@@ -67,6 +67,32 @@ repos:
     rev: v0.25
     hooks:
       - id: validate-pyproject
+  # Regenerate environment.yml from pyproject.toml when deps change (run on commit; review diff).
+  # Dev env uses python>=3.12; conda-only deps (make, pip, pymc-bart, marimo[mcp]) are in args.
+  - repo: https://github.com/usnistgov/pyproject2conda
+    rev: v0.22.1
+    hooks:
+      - id: pyproject2conda-yaml
+        name: Sync environment.yml from pyproject.toml
+        args:
+          - -e
+          - dev
+          - -o
+          - environment.yml
+          - -n
+          - CausalPy
+          - -w
+          - force
+          - --python-include
+          - "python>=3.12"
+          - -d
+          - make
+          - -d
+          - pip
+          - -d
+          - pymc-bart
+          - -r
+          - "marimo[mcp]"
   - repo: local
     hooks:
       - id: validate-bibtex

AGENTS.md

@@ -6,6 +6,9 @@ Use `mamba`, `micromamba`, or `conda` (in that preference order) to manage the `
 
 See the [python-environment skill](.github/skills/python-environment/SKILL.md) for full setup instructions: tool detection, environment creation, editable install, and troubleshooting.
 
+- Dependencies live in `pyproject.toml`; `environment.yml` is generated from it (do not edit by hand—see CONTRIBUTING). Optional: `pymc-marketing` is in the `docs` extra only.
+- **Development**: The supported setup is the conda env (`environment.yml`). `pip install -e .[dev]` works but does not include conda-only tooling (e.g. `make`, `pymc-bart`, `marimo`); do not suggest pip-only dev as equivalent.
+
 ## Testing preferences
 
 - Write all Python tests as `pytest` style functions, not unittest classes

CONTRIBUTING.md

@@ -115,7 +115,9 @@ For more instructions see the [Pull request checklist](#pull-request-checklist)
     conda env create -f environment.yml
     ```
 
-    To update an existing environment after changes to `environment.yml`:
+    **Note:** `environment.yml` is generated from `pyproject.toml` by a pre-commit hook. To change dependencies, edit `pyproject.toml` and run `pre-commit run --all-files` (or regenerate with `pyproject2conda yaml` using the same args as in `.pre-commit-config.yaml`). Do not edit `environment.yml` by hand—it will be overwritten when `pyproject.toml` is committed.
+
+    To update an existing environment after changes to `environment.yml` (e.g. after pulling or after regenerating it from `pyproject.toml`):
 
     ```bash
     conda env update --file environment.yml --prune

README.md

@@ -24,6 +24,8 @@ To get the latest release:
 pip install CausalPy
 ```
 
+If you run into installation issues with PyMC (e.g. BLAS or compilation), try the conda install: `conda install -c conda-forge causalpy`.
+
 Alternatively, if you want the very latest version of the package you can install from GitHub:
 
 ```bash

causalpy/tests/test_integration_its_new_timeseries.py

@@ -23,6 +23,9 @@
 @pytest.mark.integration
 def test_its_with_bsts_model():
     """InterruptedTimeSeries integration using BayesianBasisExpansionTimeSeries."""
+    pytest.importorskip(
+        "pymc_marketing", reason="pymc-marketing optional for default BSTS components"
+    )
     # Prepare data
     df = (
         cp.load_data("its")

causalpy/tests/test_integration_pymc_examples.py

@@ -850,6 +850,9 @@ def test_inverse_prop(mock_pymc_sample):
 @pytest.mark.integration
 def test_bayesian_structural_time_series():
     """Test the BayesianBasisExpansionTimeSeries model."""
+    pytest.importorskip(
+        "pymc_marketing", reason="pymc-marketing optional for default BSTS components"
+    )
     # Generate synthetic data
     rng = np.random.default_rng(seed=123)
     dates = pd.date_range(start="2020-01-01", end="2021-12-31", freq="D")

causalpy/tests/test_timeseries_model_coverage.py

@@ -42,6 +42,14 @@ class MockComponentNoApply:
 class TestBayesianBasisExpansionTimeSeriesCoverage:
     """Test uncovered branches in BayesianBasisExpansionTimeSeries."""
 
+    @pytest.fixture(autouse=True)
+    def _skip_if_no_pymc_marketing(self):
+        """Skip entire class when pymc-marketing not installed (needed for default BSTS components)."""
+        pytest.importorskip(
+            "pymc_marketing",
+            reason="pymc-marketing optional for default BSTS components",
+        )
+
     @pytest.fixture
     def sample_data(self):
         """Create sample time series data."""

environment.yml

@@ -1,24 +1,39 @@
+#
+# This file is autogenerated by pyproject2conda
+# with the following command:
+#
+#     $ pre-commit
+#
+# You should not manually edit this file.
+# Instead edit the corresponding pyproject.toml file.
+#
 name: CausalPy
 channels:
   - conda-forge
 dependencies:
+  - python>=3.12
   - arviz>=0.14.0
+  - codespell
   - graphviz
-  - make
+  - interrogate
   - ipython!=8.7.0
+  - make
   - matplotlib>=3.5.3
-  - numpy
+  - nbconvert
+  - nbformat
+  - numpy<2.4
   - pandas
   - patsy
   - pre-commit
+  - pymc-bart
+  - pymc-extras>=0.3.0
   - pymc>=5.15.1
   - scikit-learn>=1
   - scipy
   - seaborn>=0.11.2
   - statsmodels
+  - twine
   - xarray>=v2022.11.0
-  - pymc-extras>=0.3.0
-  - pymc-bart
-  - python>=3.12
   - pip
-  - "marimo[mcp]"
+  - pip:
+      - marimo[mcp]

pyproject.toml

@@ -47,7 +47,6 @@ dependencies = [
     "pandas",
     "patsy",
     "pymc>=5.15.1",
-    "pymc-marketing>=0.13.1",
     "scikit-learn>=1",
     "scipy",
     "seaborn>=0.11.2",
@@ -73,6 +72,7 @@ dev = [
 ]
 docs = [
     "ipykernel",
+    "pymc-marketing>=0.13.1",
     "daft-pgm",
     "linkify-it-py",
     "myst-nb<=1.0.0",
@@ -95,6 +95,9 @@ docs = [
 lint = ["interrogate", "pre-commit", "ruff", "mypy"]
 test = ["pytest", "pytest-cov", "codespell", "nbformat", "nbconvert", "papermill"]
 
+[tool.pyproject2conda]
+channels = ["conda-forge"]
+
 [project.urls]
 Homepage = "https://github.com/pymc-labs/CausalPy"
 "Bug Reports" = "https://github.com/pymc-labs/CausalPy/issues"