update version for pypi, combine dev and test dependencies, remove un…

…needed files (#148) * only publish to testPyPi when changing the tag since upload fails with duplicate name * remove extra files * fix SALib depreciation warning * combine dev and test dependencies, update docs (#144) * remove unused test_model.py file (#145) * update tag version, consolidate test dependencies to dev (#147) Co-authored-by: Travis Thurber <[email protected]> --------- Co-authored-by: Travis Thurber <[email protected]>
IMMM-SFA · Mar 3, 2025 · c06cf89 · c06cf89
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diff --git a/.github/workflows/04_publish-to-pypi.yml b/.github/workflows/04_publish-to-pypi.yml
@@ -101,6 +101,7 @@ jobs:
 
   publish-to-testpypi:
     name: Publish to TestPyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to test PyPI on tag pushes
     needs:
     - build
     runs-on: ubuntu-latest

diff --git a/docs/source/A2.2_saltelli.rst b/docs/source/A2.2_saltelli.rst
@@ -45,7 +45,7 @@ walkthrough.
     # Import relevant libraries
     import matplotlib.pyplot as plt
 
-    from SALib.sample import saltelli
+    import SALib.sample.sobol as sobol_sample
     from SALib.analyze import sobol
     from SALib.test_functions import Ishigami
 
@@ -85,8 +85,9 @@ resulting Saltelli sample.
 
 .. code:: ipython3
 
-    #Generate parmeter values using the saltelli.sample function
-    param_values = saltelli.sample(problem, 256)
+    # Generate parmeter values using the saltelli.sample function
+    param_values = sobol_sample.sample(problem, 256)
+
 
     print(f"`param_values` shape:  {param_values.shape}")
 
@@ -98,7 +99,7 @@ resulting Saltelli sample.
 
 .. code:: ipython3
 
-    #Plot the 2048 samples of the parameters
+    # Plot the 2048 samples of the parameters
 
     fig = plt.figure(figsize = (7, 5))
     ax = plt.axes(projection ="3d")

diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst
@@ -48,7 +48,7 @@ The following is the recommended workflow for contributing:
       pre-commit install
 
 
-1. Add your changes and commit them:
+3. Add your changes and commit them:
 
   .. code-block:: bash
 
@@ -57,18 +57,22 @@ The following is the recommended workflow for contributing:
     git commit -m "<my short message>"
 
 
-1. Ensure all tests pass:
+4. Ensure all 
 
-    Ensure your tests pass locally before pushing to your remote branch where GitHub actions will launch CI services to build the package, run the test suite, and evaluate code coverage. To do this, ensure that ``pytest`` has been installed then navigate to the root of your cloned directory (e.g., <my-path>/msd_uncertainty_ebook) and run ``pytest`` in the terminal.
 
-  .. code-block:: bash
+s pass:
+
+  Ensure your tests pass locally before pushing to your remote branch where GitHub actions will launch CI services to build the package, run the test suite, and evaluate code coverage. To do this, ensure that ``pytest`` is installed then navigate to the root of your cloned directory (e.g., <my-path>/msd_uncertainty_ebook) and run ``pytest`` in the terminal.
 
-      pip install -e ".[test]"
+  .. code-block:: bash
 
+      pip install -e ".[dev]"
       pytest
 
 
-  Changes to the documentation can be made in the ``msd_uncertainty_ebook/docs/source`` directory containing the RST files. To view your changes, ensure you have the development dependencies of **msd_uncertainty_ebook** installed and run the following from the ``msd_uncertainty_ebook/docs/source`` directory:
+5. Update the Documentation:
+
+  Changes to the documentation can be made in the ``msd_uncertainty_ebook/docs/source`` directory containing the RST files. To view your changes, ensure you have the documentation dependencies of **msd_uncertainty_ebook** installed and run the following from the ``msd_uncertainty_ebook/docs/source`` directory:
 
   .. code-block:: bash
 
@@ -79,13 +83,13 @@ The following is the recommended workflow for contributing:
 
   This will generate your new documentation in a directory named ``msd_uncertainty_ebook/docs/build/html``. You can open the ``index.html`` in your browser to view the documentation site locally. If your changes are merged into the main branch of **msd_uncertainty_ebook**, changes in your documentation will go live on the `uc-ebook.org documentation <https://uc-ebook.org/docs/html/index.html>`_. If your changes are merged into the dev branch of **msd_uncertainty_ebook**, changes in your documentation will go live on the `dev site <https://uc-ebook.org/dev/docs/html/index.html>`_.
 
-1. Push your changes to the remote
+6. Push your changes to the remote
 
   .. code-block:: bash
 
     git push origin <my-branch-name>
 
 
-4. Submit a pull request with the submission `template <https://github.com/IMMM-SFA/msd_uncertainty_ebook/blob/main/.github/PULL_REQUEST_TEMPLATE/contribution_checklist.md>`_ copied into the pull request description and filled out.
+7. Submit a pull request with the submission `template <https://github.com/IMMM-SFA/msd_uncertainty_ebook/blob/main/.github/PULL_REQUEST_TEMPLATE/contribution_checklist.md>`_ copied into the pull request description and filled out.
 
-5. If approved, your pull request will be merged first into the dev, and then into the main branch by a **msd_uncertainty_ebook** admin and a release will be conducted subsequently. **msd_uncertainty_ebook** uses `semantic naming <https://semver.org/>`_ for versioned releases. Each release receives a DOI via a linked Zenodo service automatically.
+8. If approved, your pull request will be merged first into the dev, and then into the main branch by a **msd_uncertainty_ebook** admin and a release will be conducted subsequently. **msd_uncertainty_ebook** uses `semantic naming <https://semver.org/>`_ for versioned releases. Each release receives a DOI via a linked Zenodo service automatically.
diff --git a/msdbook/model.py b/msdbook/model.py
diff --git a/msdbook/tests/test_model.py b/msdbook/tests/test_model.py
diff --git a/notebooks/functions/readme b/notebooks/functions/readme
diff --git a/notebooks/sa_saltelli_sobol_ishigami.ipynb b/notebooks/sa_saltelli_sobol_ishigami.ipynb
diff --git a/pyproject.toml b/pyproject.toml
@@ -10,13 +10,14 @@ msdbook = ["*.txt", "*.csv", "*.npy", "*.resultfile"]
 
 [project]
 name = "msdbook"
-version = "0.1.5"
+version = "0.1.6"
 description = "Jupyter notebook support for the MSD uncertainty ebook."
 readme = "README.md"
-requires-python = ">=3.9, <3.13"
+requires-python = ">=3.9"
 keywords = ["uncertainty characterization", "MSD", "MultiSector Dynamics"]
 authors = [
   { name="Chris R. Vernon", email="[email protected]" },
+  { name="Travis Thurber", email="[email protected]" },
   { name="Em Rexer", email="[email protected]" },
 ]
 
@@ -48,6 +49,8 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
     "pre-commit>=3.7.1",
+    "pytest>=7.0.0",
+    "pytest-mock>=3.10",
 ]
 
 docs = [
@@ -63,11 +66,6 @@ docs = [
     "twine>=3.4.1",
 ]
 
-test = [
-    "pytest>=7.0.0",
-    "pytest-mock>=3.10",
-]
-
 [project.urls]
 Homepage = "https://uc-ebook.org/"
 Repository = "https://github.com/IMMM-SFA/msd_uncertainty_ebook"