Replaces PyTables with H5PY as the HDF5 interface

.github/workflows/ci.yml

@@ -0,0 +1,65 @@
+name: Python package
+
+on:
+  push:
+    branches:
+      - 'master'
+  pull_request:
+
+
+jobs:
+  lint-coverage:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Lint
+        run: uv run --python ${{ matrix.python-version }} --extra dev ruff check --output-format=github
+
+      - name: Generate coverage report
+        run: |
+          uv run --python ${{ matrix.python-version }} --extra dev \
+            pytest tests/ \
+            --cov=. \
+            --cov-branch \
+            --cov-report=term-missing \
+            --cov-report=html:cov_html \
+            --cov-report=markdown-append:$GITHUB_STEP_SUMMARY \
+            --verbose
+
+      - uses: actions/upload-artifact@v6
+        with:
+          name: html-coverage-artifact
+          path: ./cov_html/
+
+  test:
+    needs: lint-coverage
+    runs-on: ${{ matrix.os }}
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.os }}-${{ matrix.python-version }}
+      cancel-in-progress: true
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        exclude:
+          - os: macos-latest
+            python-version: "3.9"
+          - os: macos-latest
+            python-version: "3.10"
+
+    steps:
+    - uses: actions/checkout@v6
+
+    - name: Setup uv
+      uses: astral-sh/setup-uv@v7
+
+    - name: Install and test
+      run: uv run --python ${{ matrix.python-version }} --extra dev pytest

.gitignore

@@ -21,3 +21,9 @@ nosetests.xml
 
 # Python build directory
 api/python/build
+
+.venv/
+venv/
+pyenv/
+.idea/
+build/

CHANGES.txt

@@ -6,4 +6,5 @@ v0.3.3, 2017-03-07 -- Python 3 compatible
 v0.3.4, 2018-04-05 -- Fix incorrect version being saved
 v0.3.4.1, 2018-10-19 -- python3 compatible next for generator
 v0.3.5, 2019-12-21 -- add validator and clean-up repo structure
+v0.4.0, 2025-12-21 -- Replaces PyTables with H5Py, cleans repo structure, adds CI
 

example/python-omx-sample.py

@@ -3,36 +3,35 @@
 import numpy as np
 
 # Create some data
-ones = np.ones((100,100))
-twos = 2.0*ones
+ones = np.ones((100, 100))
+twos = 2.0 * ones
 
 
 # Create an OMX file (will overwrite existing file!)
-print('Creating myfile.omx')
-myfile = omx.open_file('myfile.omx','w')   # use 'a' to append/edit an existing file
+print("Creating myfile.omx")
+myfile = omx.open_file("myfile.omx", "w")  # use 'a' to append/edit an existing file
 
 
 # Write to the file.
-myfile['m1'] = ones
-myfile['m2'] = twos
-myfile['m3'] = ones + twos           # numpy array math is fast
+myfile["m1"] = ones
+myfile["m2"] = twos
+myfile["m3"] = ones + twos  # numpy array math is fast
 myfile.close()
 
 
 # Open an OMX file for reading only
-print('Reading myfile.omx')
-myfile = omx.open_file('myfile.omx')
+print("Reading myfile.omx")
+myfile = omx.open_file("myfile.omx")
 
-print ('Shape:', myfile.shape())                 # (100,100)
-print ('Number of tables:', len(myfile))         # 3
-print ('Table names:', myfile.list_matrices())   # ['m1','m2',',m3']
+print("Shape:", myfile.shape())  # (100,100)
+print("Number of tables:", len(myfile))  # 3
+print("Table names:", myfile.list_matrices())  # ['m1','m2',',m3']
 
 
 # Work with data. Pass a string to select matrix by name:
 # -------------------------------------------------------
-m1 = myfile['m1']
-m2 = myfile['m2']
-m3 = myfile['m3']
+m1 = myfile["m1"]
+m2 = myfile["m2"]
 
 # halves = m1 * 0.5  # CRASH!  Don't modify an OMX object directly.
 #                    # Create a new numpy array, and then edit it.
@@ -46,43 +45,42 @@
 
 # FANCY: Use attributes to find matrices
 # --------------------------------------
-myfile.close()                            # was opened read-only, so let's reopen.
-myfile = omx.open_file('myfile.omx','a')  # append mode: read/write existing file
+myfile.close()  # was opened read-only, so let's reopen.
+myfile = omx.open_file("myfile.omx", "a")  # append mode: read/write existing file
 
-myfile['m1'].attrs.timeperiod = 'am'
-myfile['m1'].attrs.mode = 'hwy'
+myfile["m1"].attrs.timeperiod = "am"
+myfile["m1"].attrs.mode = "hwy"
 
-myfile['m2'].attrs.timeperiod = 'md'
+myfile["m2"].attrs.timeperiod = "md"
 
-myfile['m3'].attrs.timeperiod = 'am'
-myfile['m3'].attrs.mode = 'trn'
+myfile["m3"].attrs.timeperiod = "am"
+myfile["m3"].attrs.mode = "trn"
 
-print('attributes:', myfile.list_all_attributes())       # ['mode','timeperiod']
+print("attributes:", myfile.list_all_attributes())  # ['mode','timeperiod']
 
 # Use a DICT to select matrices via attributes:
 
-all_am_trips = myfile[ {'timeperiod':'am'} ]                    # [m1,m3]
-all_hwy_trips = myfile[ {'mode':'hwy'} ]                        # [m1]
-all_am_trn_trips = myfile[ {'mode':'trn','timeperiod':'am'} ]   # [m3]
+all_am_trips = myfile[{"timeperiod": "am"}]  # [m1,m3]
+all_hwy_trips = myfile[{"mode": "hwy"}]  # [m1]
+all_am_trn_trips = myfile[{"mode": "trn", "timeperiod": "am"}]  # [m3]
 
-print('sum of some tables:', np.sum(all_am_trips))
+print("sum of some tables:", np.sum(all_am_trips))
 
 
 # SUPER FANCY: Create a mapping to use TAZ numbers instead of matrix offsets
 # --------------------------------------------------------------------------
 # (any mapping would work, such as a mapping with large gaps between zone
 #  numbers. For this simple case we'll just assume TAZ numbers are 1-100.)
 
-taz_equivs = np.arange(1,101)                  # 1-100 inclusive
+taz_equivs = np.arange(1, 101)  # 1-100 inclusive
 
-myfile.create_mapping('taz', taz_equivs)
-print('mappings:', myfile.list_mappings())                 # ['taz']
+myfile.create_mapping("taz", taz_equivs)
+print("mappings:", myfile.list_mappings())  # ['taz']
 
-tazs = myfile.mapping('taz')          # Returns a dict:  {1:0, 2:1, 3:2, ..., 100:99}
+tazs = myfile.mapping("taz")  # Returns a dict:  {1:0, 2:1, 3:2, ..., 100:99}
 
-m3 = myfile['m3']
+m3 = myfile["m3"]
 
-print('cell value:', m3[tazs[100]][tazs[100]])      # 3.0  (taz (100,100) is cell [99][99])
+print("cell value:", m3[tazs[100]][tazs[100]])  # 3.0  (taz (100,100) is cell [99][99])
 
 myfile.close()
-