Merge pull request #167 from respec/develop

Merge Develop in Main in preparation for new release

Author: PaulDudaRESPEC

.github/workflows/hsp2-pip-install-test.yml

@@ -0,0 +1,87 @@
+name: Python application
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master", "develop", "develop-specact" ]
+
+permissions:
+  contents: read
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          pip install flake8
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --ignore=F821 --show-source --statistics --exclude=build/*
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+  
+  test-pytest:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        pandas-version: [""]
+        include:
+          - python-version: "3.11"
+            pandas-version: "pandas>2.0"
+            coverage: true
+          - python-version: "3.11"
+            pandas-version: "pandas>1.5,<2.0"
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install hsp2
+        run: |
+          # install the hsp2 executable
+          pip install .[dev]
+      - if: ${{ matrix.pandas-version }}
+        run: pip install "${{ matrix.pandas-version }}"
+      - if: ${{ matrix.coverage }}
+        run: |
+          # python coverage
+          NUMBA_DISABLE_JIT=1 pytest --cov --cov-branch --cov-report term-missing
+      - if: ${{ ! matrix.coverage }}
+        run: pytest
+  
+  test-cmd:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install hsp2
+        run: |
+          # install the hsp2 executable
+          pip install .
+      - name: Run hsp2
+        run: |
+          # TODO: find much shorter test case.
+          hsp2 import_uci ./tests/test10/HSP2results/test10.uci _temp_test10.h5
+          hsp2 run _temp_test10.h5
+   

.gitignore

@@ -1,3 +1,6 @@
+# Manual
+_no_git*
+
 # Editors & IDEs
 .vscode
 .vs
@@ -42,6 +45,7 @@ htmlcov
 *.log
 *.hbnhead
 *.units.dbf
+*_temp*.h5
 
 # Translations
 *.mo
@@ -62,6 +66,11 @@ tests/GLWACSO/HSP2results/hspp007.hdf
 tests/GLWACSO/HSPFresults/hspf006.HBN
 tests/GLWACSO/HSP2results/hspp007.uci
 tests/test_report_conversion.html
-tests/land_spec/hwmA51800.h5
-tests/testcbp/HSP2results/PL3_5250_0001.h5
+
+# Omit big files
+tests/**/*.h5
 tests/testcbp/HSP2results/*.csv
+
+# R files
+.Rdata
+.Rhistory

HSP2/SPECL.py

@@ -32,21 +32,21 @@
 
 if file_ext.upper() == "UCI":
     h5_name = filename[:-3] + "h5"
-    from HSP2tools.readUCI import readUCI
+    from hsp2.hsp2tools.readUCI import readUCI
     readUCI(filename, h5_name)
     # readUCI('HSPF.uci', 'test.h5')
 
 if file_ext.upper() == "WDM":
     h5_name = filename[:-3] + "h5"
-    from HSP2tools.readWDM import readWDM
+    from hsp2.hsp2tools.readWDM import readWDM
     readWDM(filename, h5_name)
     # readWDM('GRICM.wdm', 'test.h5')
     # readWDM('ZUMBROSCEN.WDM', 'test.h5')
 
 if file_ext.upper() == ".H5":
-    from HSP2.main import main
-    from HSP2IO.hdf import HDF5
-    from HSP2IO.io import IOManager
+    from hsp2.hsp2.main import main
+    from hsp2.hsp2io.hdf import HDF5
+    from hsp2.hsp2io.io import IOManager
 
     hdf5_instance = HDF5(filename)
     io_manager = IOManager(hdf5_instance)