Add pytest to deps and CI

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

@@ -1,6 +1,5 @@
 name: Python application
-# this is a standard setup copied from
-# https://docs.github.com/en/enterprise-server@3.10/actions/automating-builds-and-tests/building-and-testing-python
+
 on:
   push:
     branches: [ "master" ]
@@ -11,37 +10,78 @@ permissions:
   contents: read
 
 jobs:
-  build:
+  lint:
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.10"
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-        pip install mando numba pandas tables
-    - name: Install hsp2
-      run: |
-        # install the hsp2 executable
-        pip install .
-    - 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=HSP2/ACIDPH.py,build/lib/HSP2/ACIDPH.py
-        # 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
-    - name: Test with pytest
-      run: |
-        pytest tests/ptest/test_sysexit.py
-        # add additional test, ex:
-        # pytest tests/testcbp/HSP2results/benchmark.py
-    - name: Run hsp2 test10
-      run: |
-        cd tests/test10/HSP2results
-        hsp2 import_uci test10.uci test10.h5
-        hsp2 run test10.h5
+      - 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

HSP2/ADCALC.py

@@ -109,10 +109,10 @@ def _adcalc_(ui, ts):
 		for index in range(nexits):
 			ts['EOVOL' + str(index + 1)] = EOVOL[:, index]
 
-	ROS = ui['ROS']
+	ROS = ui.get('ROS', 0.0)
 	OS  = zeros(nexits)
 	for index in range(nexits):
-		OS[index] = ui['OS' + str(index + 1)]
+		OS[index] = ui.get('OS' + str(index + 1), 0.0)
 
 	# external time series
 	O = zeros((simlen, nexits))

HSP2/GENER.py

@@ -10,9 +10,9 @@ class Gener():
     """
 
     def __init__(self, segment: str, siminfo: Dict, copies: Dict, geners: Dict, ddlinks: Dict, ddmasslinks: Dict, tsin: Dict, ddgener: Dict) -> None:
-        self.ts_input_1 = pd.Series() # type: pd.Series
-        self. ts_input_2 = pd.Series() # type: pd.Series
-        self.ts_output = pd.Series()  # type: pd.Series
+        self.ts_input_1 = pd.Series(dtype="float64")  # type: pd.Series
+        self.ts_input_2 = pd.Series(dtype="float64")  # type: pd.Series
+        self.ts_output = pd.Series(dtype="float64")  # type: pd.Series
         self.opcode = 0               # type: int
         self.k = -1.0E30              # type: float 
 
@@ -27,7 +27,7 @@ def __init__(self, segment: str, siminfo: Dict, copies: Dict, geners: Dict, ddli
             self.ts_input_1 = ts
 
         for link in ddlinks[segment]:
-            ts = pd.Series()
+            ts = pd.Series(dtype="float64")
             if link.SVOL == 'COPY': 
                 copy = copies[link.SVOLNO]
                 ts = copy.get_ts(link.SMEMN,link.SMEMSB1)

HSP2/OXRX_Class.py

@@ -129,17 +129,20 @@ def __init__(self, siminfo, nexits, vol, ui_rq, ui, ts):
 		self.expred = 0.0; self.exprev = 0.0
 		self.expod = 0.0; self.exprel = 0.0
 
+		self.len_ = ui['LEN'] * 5280.0  # mi to feet
+		if self.uunits == 2:
+			self.len_ = ui['LEN'] * 1000.0  # length of reach, in meters
+
 		if self.LKFG == 1:
 			self.cforea = ui['CFOREA']	 # reaeration parameter from table-type ox-cforea
+			self.tcginv = 0
 
 		elif self.REAMFG == 1:			 # tsivoglou method;  table-type ox-tsivoglou
 			self.reakt	= ui['REAKT']
 			self.tcginv = ui['TCGINV']
-
-			self.len_	= ui['LEN'] * 5280.0  # mi to feet
+
 			self.delth	= ui['DELTH']
 			if self.uunits == 2:
-				self.len_ = ui['LEN'] * 1000.0  # length of reach, in meters
 				self.delth = ui['DELTH'] * 1000.0  # convert to meters
 
 		elif self.REAMFG == 2:			# owen/churchill/o'connor-dobbins; table-type ox-tcginv

HSP2/__init__.py

@@ -2,9 +2,11 @@
 Authors: Robert Heaphy, Ph.D. and Paul Duda
 License: LGPL2
 '''
+from importlib.metadata import version
 
 from HSP2.main import main
 from HSP2.mainDoE import main as mainDoE
 from HSP2.utilities import versions, flowtype
-from _version import __version__
+
+__version__ = version("hsp2")