Remove all automatic installation of cmdstan from the package.

Now the package is distributed as pure python package, which should ease distribution. Instructions to use the stan model will be added in later commit.

Author: viktorht

.github/workflows/build-wheels.yaml

@@ -12,35 +12,29 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ["macos-latest"] #, "ubuntu-latest", "windows-latest"]
+        os: ["macos-latest", "ubuntu-latest", "windows-latest"]
       fail-fast: false
 
     steps:
       - name: "Checkout repo"
         uses: actions/checkout@v4
 
-      - name: "Build wheels"
-        uses: pypa/cibuildwheel@v2.8.1
+      - name: "Set up Python"
+        uses: actions/setup-python@v5
         with:
-          package-dir: .
+          python-version: '3.10'
 
-        env:
-          CIBW_ENVIRONMENT: >
-            PSEUDOBATCH_REPACKAGE_CMDSTAN=TRUE
+      - name: "Install build"
+        run: python -m pip install build
 
-          CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
-          CIBW_BUILD: cp37-* cp38-* cp39-* cp310-*
-          CIBW_SKIP: "*musllinux*"
-          CIBW_ARCHS: native
-          CIBW_BUILD_FRONTEND: build
-          # CIBW_TEST_REQUIRES: pytest
-          # CIBW_TEST_COMMAND: "pytest {project}/tests"
+      - name: "Build wheels"
+        run: python -m build --wheel --outdir dist
 
       - name: "Upload wheel as artifact"
         uses: actions/upload-artifact@v4
         with:
           name: artifact-${{ matrix.os }}-wheel
-          path: "./**/*.whl"
+          path: "./dist/*.whl"
 
   make-sdist:
     name: Make source distribution

.github/workflows/documentation.yaml

@@ -5,7 +5,7 @@ permissions:
 
 env:
   GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-  CMDSTAN_VERSION: "2.31.0" 
+  CMDSTAN_VERSION: "2.33.0" 
 
 jobs:
   docs:
@@ -16,7 +16,7 @@ jobs:
       - name: Install cmdstanpy
         run: |
           python -m pip install --upgrade pip wheel
-          pip install "cmdstanpy==1.0.4"
+          pip install "cmdstanpy==1.1.0"
       - name: CmdStan installation cacheing
         uses: actions/cache@v2
         with:

.github/workflows/main.yaml

@@ -13,7 +13,7 @@ on:
   workflow_dispatch: {}
 
 env:
-  CMDSTAN_VERSION: "2.31.0"
+  CMDSTAN_VERSION: "2.33.0"
 
 jobs:
   sk-stan-learn:
@@ -35,7 +35,7 @@ jobs:
       - name: Install cmdstanpy
         run: |
           python -m pip install --upgrade pip wheel
-          pip install "cmdstanpy==1.0.4"
+          pip install "cmdstanpy==1.1.0"
 
       - name: CmdStan installation cacheing
         uses: actions/cache@v2

pseudobatch/error_propagation/__init__.py

@@ -16,53 +16,14 @@
     cmdstanpy_installed = False
     raise ImportError(
         "cmdstanpy is not installed. To use the error propagation module, "
-        "please install cmdstanpy by running 'pip install cmdstanpy'. "
-        "Then install the CmdStan binaries by running 'cmdstanpy.install_cmdstan()'. "
-        "Finally, install the remaining dependencies for the error propagation module "
-        "by running 'pip install pseudobatch[error_propagation]'."
+        "please install cmdstanpy and CmdStan. You can find installation instructions "
+        "for different setups at https://mc-stan.org/cmdstanpy/installation.html."
+        "After installing cmdstanpy and CmdStan install the remaining dependencies "
+        "for the error propagation module by running "
+        "'pip install pseudobatch[error_propagation]'."
     )
 
 if cmdstanpy_installed:
     from pseudobatch.error_propagation.error_propagation import (
         run_error_propagation,
     )
-
-    STAN_FILES_FOLDER = Path(__file__).parent / "stan"
-    CMDSTAN_VERSION = "2.31.0"
-
-    # on Windows specifically, we should point cmdstanpy to the repackaged
-    # CmdStan if it exists. This lets cmdstanpy handle the TBB path for us.
-    local_cmdstan = STAN_FILES_FOLDER / f"cmdstan-{CMDSTAN_VERSION}"
-    if local_cmdstan.exists():
-        cmdstanpy.set_cmdstan_path(str(local_cmdstan.resolve()))
-
-    def load_stan_model(name: str) -> cmdstanpy.CmdStanModel:
-        """
-        Try to load precompiled Stan models. If that fails,
-        compile them.
-        """
-        try:
-            model = cmdstanpy.CmdStanModel(
-                exe_file=STAN_FILES_FOLDER / f"{name}.exe",
-                stan_file=STAN_FILES_FOLDER / f"{name}.stan",
-                compile=False,
-            )
-        except ValueError:
-            warnings.warn(
-                f"Failed to load pre-built model '{name}.exe', compiling"
-            )
-            model = cmdstanpy.CmdStanModel(
-                stan_file=STAN_FILES_FOLDER / f"{name}.stan",
-                stanc_options={"O1": True},
-            )
-            shutil.copy(
-                model.exe_file,  # type: ignore
-                STAN_FILES_FOLDER / f"{name}.exe",
-            )
-
-        return model
-
-    ERROR_PROPAGATION = load_stan_model("error_propagation")
-
-    # example: just print the info of the model
-    print(ERROR_PROPAGATION.exe_info())

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools", "wheel", "cmdstanpy==1.1.0"]
+requires = ["setuptools", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [tool.isort]