Refactor code structure for improved readability and maintainability

Author: dwr-psandhu

.github/workflows/docs.yml

@@ -16,16 +16,16 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.13
         uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.13"
 
       - name: Install Miniconda
         uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
-          python-version: "3.11"
+          python-version: "3.13"
           channels: conda-forge,cadwr-dms,nodefaults
           channel-priority: strict
 

.github/workflows/python-package-conda.yml

@@ -12,10 +12,10 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
-    - name: Set up Python 3.11
+    - name: Set up Python 3.13
       uses: actions/setup-python@v4
       with:
-        python-version: 3.11
+        python-version: 3.13
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
@@ -24,7 +24,7 @@ jobs:
       env:
         ANACONDA_CHANNEL_UPLOAD_TOKEN: ${{ secrets.ANACONDA_CHANNEL_UPLOAD_TOKEN }}
       run: |
-        conda create -n test_pydsm -y conda-build conda-verify numpy anaconda-client
+        conda create -n test_pydsm -y conda-build conda-verify numpy anaconda-client setuptools_scm
         source $CONDA/etc/profile.d/conda.sh
         conda activate test_pydsm
         conda config --set anaconda_upload yes

HISTORY.rst

@@ -2,6 +2,26 @@
 History
 =======
 
+Unreleased (since 2025.07.29)
+------------------------------
+* Massive refactor: reorganised package into ``pydsm.input``, ``pydsm.output``,
+  ``pydsm.analysis``, and ``pydsm.viz`` sub-packages
+* Replaced stale ``.pkl`` test fixtures with Parquet files (via pyarrow);
+  added ``--regen-fixtures`` pytest option
+* Added ``pydsm.input.xsection`` module for adjusting channel cross-section
+  properties (bottom elevation, wetted perimeter, width)
+* Added ``pydsm.output.create_gtm_restart`` for GTM restart file creation
+* Enhanced ``csv_to_dss`` CLI command with additional options
+* Parser: deterministic dtype handling; postprocessor error-handling improvements
+* Added ``README.md`` (converted from RST), ``README-dev.md`` developer guide
+* Added GitHub Actions workflow for building and deploying Sphinx docs to
+  ``gh-pages``; docs now use nbsphinx with pre-executed notebooks
+* Updated ``environment.yml`` (core + viz), ``environment_dev.yml``
+  (core + viz + test), ``environment-docs.yml`` (full) to align with
+  ``pyproject.toml`` optional-dependency groups
+* Added ``myst-parser`` support so Sphinx can include Markdown source files
+* Fixed pandas 2.x / numpy 2.x compatibility in notebooks and test fixtures
+
 2021.12.13
 ----------
 Added major functionality for hydro and qual .h5 reading

README.md

@@ -47,21 +47,3 @@ pip install "pydsm[dev]"   # test + docs tools
 ```
 
 ---
-
-## Known Issues
-
-`conda install h5py` lacks szip/zlib support
-([upstream issue](https://github.com/ContinuumIO/anaconda-issues/issues/11382)).
-Workaround:
-
-```bash
-conda uninstall h5py
-pip install h5py
-```
-
----
-
-## Credits
-
-This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter)
-and the [audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage) project template.

conda.recipe/meta.yaml

@@ -16,8 +16,6 @@ build:
   script_env:
    - SETUPTOOLS_SCM_PRETEND_VERSION
   script: {{ PYTHON }} -m pip install --no-build-isolation --no-deps --ignore-installed -vv .
-  noarch: python
-  number: 0
   entry_points:
     {% for name, reference in project['scripts'].items() %}
     - {{ name }} = {{ reference }}
@@ -42,11 +40,9 @@ requirements:
     source_files:
       - tests
     requires:
-      - pytest
-      - pytest-cov
-    {% for dep in project.get("optional-dependencies", {}).get('test', []) %}
-    - {{ dep.lower() }}
-    {% endfor %}
+      {% for dep in project.get("optional-dependencies", {}).get('test', []) %}
+      - {{ dep.lower() }}
+      {% endfor %}
     commands:
       - (setlocal && cd tests && pytest && endlocal) # [win]
       - (cd tests; pytest) # [unix]

environment-docs.yml

@@ -13,7 +13,7 @@ channels:
   - cadwr-dms
   - nodefaults
 dependencies:
-  - python=3.11
+  - python=3.13
   - pip
   # --- core runtime (mirrors pyproject.toml [project.dependencies]) ---
   - click

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "pydsm"
 description = "For loading data from DSM2 hdf5 files into pandas DataFrame"
-readme = "README.rst"
+readme = "README.md"
 authors = [
     {name = "Nicky Sandhu", email = "psandhu@water.ca.gov"},
 ]
@@ -89,4 +89,32 @@ dev = [
     "coverage",
     "twine",
     "setuptools_scm>=6.2",
+    "towncrier",
 ]
+
+[tool.towncrier]
+filename = "HISTORY.rst"
+directory = "changelog.d"
+title_format = "{version} ({project_date})"
+issue_format = "`#{issue} <https://github.com/CADWRDeltaModeling/pydsm/issues/{issue}>`_"
+underlines = ["-", "~", "^"]
+
+[[tool.towncrier.type]]
+directory = "feat"
+name = "New Features"
+showcontent = true
+
+[[tool.towncrier.type]]
+directory = "fix"
+name = "Bug Fixes"
+showcontent = true
+
+[[tool.towncrier.type]]
+directory = "docs"
+name = "Documentation"
+showcontent = true
+
+[[tool.towncrier.type]]
+directory = "misc"
+name = "Miscellaneous"
+showcontent = true