Add regression testing continuous integration.

sandialabs · Sep 9, 2024 · e4ec14f · e4ec14f
1 parent 440d617
commit e4ec14f
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diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
@@ -0,0 +1,81 @@
+name: Continuous Integration
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+
+      - name: Harden Runner
+        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
+        with:
+          egress-policy: audit
+
+      - name: Check out the commit
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ~${{ matrix.version }}
+
+      - name: Install development dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install -r requirements.txt
+
+      - name: Test install
+        run: python3 -m pip install .[test,dev,docs]
+
+      - name: Test with pytest
+        run: python3 -m pytest --cov=src\python\sansmic examples/ tests/
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+    #   - name: Check documentation coverage
+    #     run: |
+    #       make coverage
+    #       mv build/coverage/python.txt ../docs-coverage-report-${{ matrix.version }}.txt
+    #     working-directory: ./docs
+
+    #   - name: Archive documentation coverage results
+    #     uses: actions/upload-artifact@v3
+    #     with:
+    #       name: docs-coverage-report-${{ matrix.version }}
+    #       path: docs-coverage-report-${{ matrix.version }}.txt
+
+      - name: Test uninstall
+        run: python3 -m pip uninstall -y my-repository-name
+
+  commits:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
+        with:
+          egress-policy: audit
+
+      - name: Conventional Commits
+        uses: taskmedia/action-conventional-commits@9148865058f63a6cb560ff4bfd7d534505f43646 # v1.1.3
+        with:
+          types: >
+            build|chore|ci|docs|feat|fix|minor|patch|perf|style|refactor|test
diff --git a/docs/conf.py b/docs/conf.py
@@ -149,7 +149,7 @@
     breathe_domain_by_extension = {"hpp": "cpp"}
     breathe_projects_source = {
         "libsansmic": (
-            "../src/ext_modules/libsansmic",
+            "",
             glob.glob("../src/ext_modules/libsansmic/*"),
         )
     }

diff --git a/pyproject.toml b/pyproject.toml
@@ -29,7 +29,7 @@ classifiers = [
 [project.optional-dependencies]
 formats = ['h5py', 'openpyxl', 'tabulate']
 docs = ['Sphinx', 'pydata-sphinx-theme', 'sphinx_design', 'sphinxcontrib-bibtex', 'breathe', 'exhale', 'sphinx-argparse']
-test = ['unittest']
+test = ['unittest', 'pytest', 'pytest-cov', 'black']
 dev = ['pre-commit', 'pyproject_hooks', 'black', 'pybind11']
 
 [project.urls]

diff --git a/requirements.txt b/requirements.txt
@@ -2,3 +2,7 @@ numpy
 pandas
 pyyaml
 pre-commit
+pytest
+pytest-cov
+black
+pybind11
diff --git a/src/python/sansmic/app.py b/src/python/sansmic/app.py
@@ -335,7 +335,7 @@ def convert():
     args = parser.parse_args()
     infile = args.infile
     logger.debug("Running sansmic-convert")
-    model = sio.read_scenario(infile, warn=not args.quiet)
+    model = sio.read_scenario(infile)
     logger.debug("Successfully created scenario from {}".format(infile))
     sio.write_scenario(model, args.outfile, redundant=args.full)
     logger.debug("Successfully wrote scenario to {}".format(args.outfile))
diff --git a/src/python/sansmic/model.py b/src/python/sansmic/model.py
@@ -653,11 +653,13 @@ def _to_cstage(self, defaults=None) -> _ext.CStage:
                         (self.injection_duration + self.rest_duration) / stage.timestep
                     )
                 )
-        elif self.save_frequency is not None:
-            stage.print_interval = self.save_frequency
+            else:
+                stage.print_interval = int(self.save_frequency)
+        elif isinstance(self.save_frequency, (int, float)):
+            stage.print_interval = int(self.save_frequency)
         else:
             stage.print_interval = defaults.get(
-                "solver_timestep", int(np.round(24.0 / stage.timestep))
+                "save_frequency", int(np.round(24.0 / stage.timestep))
             )
         stage.subsequent = 0 if self.set_initial_conditions else 1
         stage.rest_duration = self.rest_duration

diff --git a/tests/baseline.dat b/tests/baseline.dat
@@ -1,6 +1,6 @@
-Ordinary leaching - direct
-100	0	2400	0	0	600	1	0	0
-1000.   32.0  680.0	700.0   20.0
+Witdrawal leaching - initial
+100	1	12000	0	0	480	1	0	0
+1000.   32.0  1000.0	350.0   20.0
 240000.0
 4.925	5.3750	4.925	5.3750
 1.03	1.2019
@@ -108,28 +108,28 @@ Ordinary leaching - direct
 2
 2
 1.0   0.05   4000.   4000.
-Ordinary leaching - reverse
-100	0	2400	1	0	600	1	0	0
-1000.   680.0	32.0  0.0   20.0
+Ordinary leaching - direct
+100	0	12000	1	0	480	1	0	0
+1000.   32.0  600.0	0.0   20.0
 240000.0
 4.925	5.3750	4.925	5.3750
 1.03	0.0
 0.01    120
 0.0	0.0	0.0
-Leach fill
-100	2	2400	1	0	600	1	0	0
-1000.   480.0	32.0  0.0   20.0
+Ordinary leaching - reverse
+100	0	12000	1	0	480	1	0	0
+1000.   600.0	32.0  0.0   20.0
 240000.0
 4.925	5.3750	4.925	5.3750
 1.03	0.0
 0.01    120
-240000.0	0.0	0.0
-Withdrawal leaching
-100	1	2400	1	0	600	1	0	0
-1000.   680.0	32.0  0.0   20.0
+0.0	0.0	0.0
+Leach fill
+100	2	12000	1	0	480	1	0	0
+1000.   32.0	350.0  0.0   20.0
 240000.0
 4.925	5.3750	4.925	5.3750
 1.03	0.0
 0.01    120
-0.0	0.0	0.0
+240000.0	0.0	0.0
 END
diff --git a/tests/baseline.ddl b/tests/baseline.ddl
@@ -0,0 +1,102 @@
+           DEPTH       R0          DRs-->
+   101   3.0000E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+   100   3.0100E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    99   3.0200E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    98   3.0300E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    97   3.0400E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    96   3.0500E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    95   3.0600E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    94   3.0700E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    93   3.0800E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    92   3.0900E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    91   3.1000E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    90   3.1100E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    89   3.1200E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    88   3.1300E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    87   3.1400E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    86   3.1500E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    85   3.1600E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    84   3.1700E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    83   3.1800E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    82   3.1900E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    81   3.2000E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    80   3.2100E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    79   3.2200E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    78   3.2300E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    77   3.2400E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    76   3.2500E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    75   3.2600E+03  2.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    74   3.2700E+03  1.0000E+01  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    73   3.2800E+03  3.5000E+01  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    72   3.2900E+03  5.0000E+01  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    71   3.3000E+03  7.5000E+01  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    70   3.3100E+03  7.5000E+01  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    69   3.3200E+03  7.5000E+01  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    68   3.3300E+03  7.5000E+01  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
+    67   3.3400E+03  7.5000E+01  1.6794E+00  3.9976E+00  1.2351E+01  1.2352E+01
+    66   3.3500E+03  7.5000E+01  1.6948E+00  3.9813E+00  1.2041E+01  1.2059E+01
+    65   3.3600E+03  7.5000E+01  1.7166E+00  4.0037E+00  1.2030E+01  1.2064E+01
+    64   3.3700E+03  7.5000E+01  1.7380E+00  4.0259E+00  1.2008E+01  1.2057E+01
+    63   3.3800E+03  7.5000E+01  1.7591E+00  4.0481E+00  1.1971E+01  1.2037E+01
+    62   3.3900E+03  7.5000E+01  1.7800E+00  4.0697E+00  1.1918E+01  1.1998E+01
+    61   3.4000E+03  7.5000E+01  1.8004E+00  4.0912E+00  1.1841E+01  1.1937E+01
+    60   3.4100E+03  7.5000E+01  1.8206E+00  4.1132E+00  1.1730E+01  1.1840E+01
+    59   3.4200E+03  7.5000E+01  1.8404E+00  4.1351E+00  1.1546E+01  1.1671E+01
+    58   3.4300E+03  7.5000E+01  1.8599E+00  4.1568E+00  1.0054E+01  1.0186E+01
+    57   3.4400E+03  7.5000E+01  1.8791E+00  4.1786E+00  9.8364E+00  9.9762E+00
+    56   3.4500E+03  7.5000E+01  1.8978E+00  4.2001E+00  9.5632E+00  9.7106E+00
+    55   3.4600E+03  7.5000E+01  1.9161E+00  4.2215E+00  9.3363E+00  9.4921E+00
+    54   3.4700E+03  7.5000E+01  1.9340E+00  4.2428E+00  9.1451E+00  9.3102E+00
+    53   3.4800E+03  7.5000E+01  1.9514E+00  4.2641E+00  8.9828E+00  9.1580E+00
+    52   3.4900E+03  7.5000E+01  1.9690E+00  4.2887E+00  8.8538E+00  9.0414E+00
+    51   3.5000E+03  7.5000E+01  2.1430E+00  4.6468E+00  9.4094E+00  9.6241E+00
+    50   3.5100E+03  8.8000E+01  2.1597E+00  4.6544E+00  9.2488E+00  9.4830E+00
+    49   3.5200E+03  8.8000E+01  2.0217E+00  4.3341E+00  8.4962E+00  8.7398E+00
+    48   3.5300E+03  8.8000E+01  2.0376E+00  4.3252E+00  8.3596E+00  8.6298E+00
+    47   3.5400E+03  8.8000E+01  2.0384E+00  4.2879E+00  8.1710E+00  8.4690E+00
+    46   3.5500E+03  8.8000E+01  2.0185E+00  4.2420E+00  7.9788E+00  8.3053E+00
+    45   3.5600E+03  8.8000E+01  2.0082E+00  4.2130E+00  7.7942E+00  8.1506E+00
+    44   3.5700E+03  8.8000E+01  2.0030E+00  4.1934E+00  7.6108E+00  7.9985E+00
+    43   3.5800E+03  8.8000E+01  2.0003E+00  4.1794E+00  7.4296E+00  7.8496E+00
+    42   3.5900E+03  8.8000E+01  1.9988E+00  4.1689E+00  7.2482E+00  7.7017E+00
+    41   3.6000E+03  8.8000E+01  1.9978E+00  4.1604E+00  7.0644E+00  7.5523E+00
+    40   3.6100E+03  8.8000E+01  1.9968E+00  4.1532E+00  6.8765E+00  9.4072E+00
+    39   3.6200E+03  8.8000E+01  1.9955E+00  4.1465E+00  6.6842E+00  9.2043E+00
+    38   3.6300E+03  8.8000E+01  1.9937E+00  4.1401E+00  6.4882E+00  9.0042E+00
+    37   3.6400E+03  8.8000E+01  1.9912E+00  4.1336E+00  6.2902E+00  8.8019E+00
+    36   3.6500E+03  8.8000E+01  1.9882E+00  4.1271E+00  6.0932E+00  8.5910E+00
+    35   3.6600E+03  8.8000E+01  1.9846E+00  4.1204E+00  5.9007E+00  8.3512E+00
+    34   3.6700E+03  8.8000E+01  1.9812E+00  4.1142E+00  5.7174E+00  8.1396E+00
+    33   3.6800E+03  8.8000E+01  1.9788E+00  4.1115E+00  5.5508E+00  7.9540E+00
+    32   3.6900E+03  8.8000E+01  2.1166E+00  4.3991E+00  5.7414E+00  8.2999E+00
+    31   3.7000E+03  1.0000E+02  2.1120E+00  4.3856E+00  5.6182E+00  8.1493E+00
+    30   3.7100E+03  1.0000E+02  1.9711E+00  4.0955E+00  5.1419E+00  7.5063E+00
+    29   3.7200E+03  1.0000E+02  1.9692E+00  4.0920E+00  5.0329E+00  7.3899E+00
+    28   3.7300E+03  1.0000E+02  1.9675E+00  4.0887E+00  4.9515E+00  7.3018E+00
+    27   3.7400E+03  1.0000E+02  1.9659E+00  4.0858E+00  4.8931E+00  7.2377E+00
+    26   3.7500E+03  1.0000E+02  1.9645E+00  4.0830E+00  4.8526E+00  7.1923E+00
+    25   3.7600E+03  1.0000E+02  1.9632E+00  4.0805E+00  4.8254E+00  7.1609E+00
+    24   3.7700E+03  1.0000E+02  1.9620E+00  4.0781E+00  4.8077E+00  7.1395E+00
+    23   3.7800E+03  1.0000E+02  1.9609E+00  4.0760E+00  4.7965E+00  7.1250E+00
+    22   3.7900E+03  1.0000E+02  1.9599E+00  4.0739E+00  4.7907E+00  7.1163E+00
+    21   3.8000E+03  1.0000E+02  1.9589E+00  4.0721E+00  4.7877E+00  7.1107E+00
+    20   3.8100E+03  1.0000E+02  1.9580E+00  4.0703E+00  4.7857E+00  7.1063E+00
+    19   3.8200E+03  1.0000E+02  1.9572E+00  4.0686E+00  4.7840E+00  7.1024E+00
+    18   3.8300E+03  1.0000E+02  1.9564E+00  4.0671E+00  4.7825E+00  7.0989E+00
+    17   3.8400E+03  1.0000E+02  1.9556E+00  4.0656E+00  4.7810E+00  7.0957E+00
+    16   3.8500E+03  1.0000E+02  1.9549E+00  4.0642E+00  4.7796E+00  7.0926E+00
+    15   3.8600E+03  1.0000E+02  1.9543E+00  4.0629E+00  4.7783E+00  7.0898E+00
+    14   3.8700E+03  1.0000E+02  1.9536E+00  4.0617E+00  4.7771E+00  7.0872E+00
+    13   3.8800E+03  1.0000E+02  1.9531E+00  4.0605E+00  4.7759E+00  7.0847E+00
+    12   3.8900E+03  1.0000E+02  1.9525E+00  4.0594E+00  4.7748E+00  7.0824E+00
+    11   3.9000E+03  1.0000E+02  1.9520E+00  4.0583E+00  4.7737E+00  7.0802E+00
+    10   3.9100E+03  1.0000E+02  1.9515E+00  4.0573E+00  4.7727E+00  7.0781E+00
+     9   3.9200E+03  1.0000E+02  1.9510E+00  4.0564E+00  4.7718E+00  7.0762E+00
+     8   3.9300E+03  1.0000E+02  1.9505E+00  4.0555E+00  4.7708E+00  7.0743E+00
+     7   3.9400E+03  1.0000E+02  1.9501E+00  4.0546E+00  4.7700E+00  7.0726E+00
+     6   3.9500E+03  1.0000E+02  1.9497E+00  4.0537E+00  4.7691E+00  7.0709E+00
+     5   3.9600E+03  1.0000E+02  1.9493E+00  4.0529E+00  4.7683E+00  7.0694E+00
+     4   3.9700E+03  1.0000E+02  1.9488E+00  4.0515E+00  4.7665E+00  7.0642E+00
+     3   3.9800E+03  1.0000E+02  1.5303E+00  3.1593E+00  3.7076E+00  5.4468E+00
+     2   3.9900E+03  7.5000E+01  9.0298E-01  1.7524E+00  1.9607E+00  2.4800E+00
+     1   4.0000E+03  1.0000E+01  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00