Update to packaging push plus fixes

.github/workflows/hsp2-conda-install-test-dev.yml

@@ -0,0 +1,48 @@
+name: Python conda dev application
+# this is a standard setup copied from
+# https://docs.github.com/en/[email protected]/actions/automating-builds-and-tests/building-and-testing-python
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master", "develop", "develop-specact" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.11"
+    - name: Install dependencies
+      run: |
+        $CONDA/bin/conda env update --name base
+        $CONDA/bin/conda install -c conda-forge --name base mando numba pandas pytables
+        $CONDA/bin/conda install flake8
+    - name: Install hsp2
+      run: |
+        # install the hsp2 executable using dev environment
+        $CONDA/bin/conda-develop ./
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        $CONDA/bin/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
+        $CONDA/bin/flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        $CONDA/bin/conda install pytest
+        $CONDA/bin/pytest tests/ptest/test_sysexit.py
+        # Add more tests here.  Example (note, benchmark takes a long time to run and could crush the free monthly 2,000 minutes during times of high activity)
+        # $CONDA/bin/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

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

@@ -0,0 +1,48 @@
+name: Python dev application
+# this is a standard setup copied from
+# https://docs.github.com/en/[email protected]/actions/automating-builds-and-tests/building-and-testing-python
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master", "develop", "develop-specact" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.11"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+        pip install flake8 pytest
+        pip install mando numba pandas tables
+    - name: Install hsp2
+      run: |
+        # install the hsp2 executable using dev environment
+        sudo pip install .[dev]
+    - 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 more tests here.  Example (note, benchmark takes a long time to run and could crush the free monthly 2,000 minutes during times of high activity)
+        # 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

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

@@ -0,0 +1,47 @@
+name: Python application
+# this is a standard setup copied from
+# https://docs.github.com/en/[email protected]/actions/automating-builds-and-tests/building-and-testing-python
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master", "develop", "develop-specact" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    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

.gitignore

@@ -62,6 +62,13 @@ tests/GLWACSO/HSP2results/hspp007.hdf
 tests/GLWACSO/HSPFresults/hspf006.HBN
 tests/GLWACSO/HSP2results/hspp007.uci
 tests/test_report_conversion.html
+
+# Omit big files
 tests/land_spec/hwmA51800.h5
 tests/testcbp/HSP2results/PL3_5250_0001.h5
 tests/testcbp/HSP2results/*.csv
+tests/test10/HSP2results/test10.h5
+
+# R files
+.Rdata
+.Rhistory

HSP2/GENER.py

@@ -9,7 +9,7 @@ class Gener():
     Currently supports OPCODES 1-7, 9-26
     """
 
-    def __init__(self, segment: str, siminfo: Dict, copies: Dict, geners: Dict, ddlinks: Dict, ddgener: Dict) -> None:
+    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
@@ -36,20 +36,48 @@ def __init__(self, segment: str, siminfo: Dict, copies: Dict, geners: Dict, ddli
                 if link.SVOLNO in geners:
                     gener = geners[link.SVOLNO]
                     ts = gener.get_ts()
-                    if link.MFACTOR != 1: ts *= link.MFACTOR
+                    if link.MFACTOR != 1 and link.MFACTOR != '': ts *= link.MFACTOR
                 else:
                     raise NotImplementedError(
                         f"Invalid SVOL. This GENER operation does not exist. '{link.SVOLNO}'")
             else:
-                raise NotImplementedError(f"Invalid SVOL. GENER module does not currently support reading TimeSeries for '{link.SVOL}'")
-
-            if link.TGRPN == 'INPUT' and link.TMEMN == 'ONE':
-                self.ts_input_1 = ts            
-            elif link.TGRPN == 'INPUT' and link.TMEMN == 'TWO':
-                self.ts_input_2 = ts
-            else:
-                raise AttributeError(f"No attribute {link.TGRPN}{link.THEMN} to assign TimeSeries. Should be either 'INPUTONE' or 'INPUTWO'")
-
+                # get timeseries from other operations
+                if 'ONE' in tsin:
+                    self.ts_input_1 = tsin['ONE']
+                if 'TWO' in tsin:
+                    self.ts_input_2 = tsin['TWO']
+                if not 'ONE' in tsin and not 'TWO' in tsin:
+                    raise NotImplementedError(f"Invalid SVOL for '{link.SVOLNO}'")
+
+            if link.SVOL == 'COPY' or link.SVOL == 'GENER':
+                if link.MLNO != '':
+                    # also have to loop thru associated masslinks
+                    mldata = ddmasslinks[link.MLNO]
+                    for dat in mldata:
+                        mfactor = dat.MFACTOR
+                        afactr = link.AFACTR
+                        factor = afactr * mfactor
+                        ts = ts * factor
+                        if dat.TMEMN == 'ONE':
+                            self.ts_input_1 = ts
+                        elif dat.TMEMN == 'TWO':
+                            self.ts_input_2 = ts
+                        else:
+                            raise AttributeError(
+                                f"No attribute {dat.THEMN} to assign TimeSeries. Should be either 'INPUTONE' or 'INPUTTWO'")
+                else:
+                    if link.TGRPN == 'INPUT' and link.TMEMN == 'ONE':
+                        self.ts_input_1 = ts
+                    elif link.TGRPN == 'INPUT' and link.TMEMN == 'TWO':
+                        self.ts_input_2 = ts
+                    else:
+                        raise AttributeError(f"No attribute {link.TGRPN}{link.THEMN} to assign TimeSeries. Should be either 'INPUTONE' or 'INPUTTWO'")
+
+        if self.opcode in [16,17,18,19,20,21,22,23]:
+            # need to have 2 input timeseries for these
+            if self.ts_input_1.size == 0 or self.ts_input_2.size == 0:
+                raise NotImplementedError(f"Need 2 input timeseries for this gener '{link.SVOLNO}'")
+
         self._execute_gener()
 
     def get_ts(self) -> pd.Series:

HSP2/PLANK_Class.py

@@ -1,3 +1,5 @@
+import os
+
 import numpy as np
 from numpy import zeros, array
 from math import log, exp
@@ -10,9 +12,16 @@
 from HSP2.RQUTIL import sink, decbal
 from HSP2.utilities  import make_numba_dict, initm
 
+if os.environ.get("NUMBA_DISABLE_JIT", 0): # jit should be on by default.
+	OXRX_Class_ = OXRX_Class
+	NUTRX_Class_ = NUTRX_Class
+else:
+	OXRX_Class_ = OXRX_Class.class_type.instance_type
+	NUTRX_Class_ = NUTRX_Class.class_type.instance_type
+
 spec = [
-	('OXRX', OXRX_Class.class_type.instance_type),
-	('NUTRX', NUTRX_Class.class_type.instance_type),
+	('OXRX', OXRX_Class_),
+	('NUTRX', NUTRX_Class_),
 	('aldh', nb.float64),
 	('aldl', nb.float64),
 	('alnpr', nb.float64),

HSP2/RQUAL_Class.py

@@ -1,3 +1,5 @@
+import os
+
 import numpy as np
 from numpy import where, zeros, array
 from math import log
@@ -10,11 +12,22 @@
 from HSP2.PHCARB_Class import PHCARB_Class
 from HSP2.utilities  import make_numba_dict, initm
 
+if os.environ.get("NUMBA_DISABLE_JIT", 0): # jit should be on by default.
+	OXRX_Class_ = OXRX_Class
+	NUTRX_Class_ = NUTRX_Class
+	PLANK_Class_ = PLANK_Class
+	PHCARB_Class_ = PHCARB_Class
+else:
+	OXRX_Class_ = OXRX_Class.class_type.instance_type
+	NUTRX_Class_ = NUTRX_Class.class_type.instance_type
+	PLANK_Class_ = PLANK_Class.class_type.instance_type
+	PHCARB_Class_ = PHCARB_Class.class_type.instance_type
+
 spec = [
-	('OXRX', OXRX_Class.class_type.instance_type),
-	('NUTRX', NUTRX_Class.class_type.instance_type),
-	('PLANK', PLANK_Class.class_type.instance_type),
-	('PHCARB', PHCARB_Class.class_type.instance_type),
+	('OXRX', OXRX_Class_),#.class_type.instance_type),
+	('NUTRX', NUTRX_Class_),#.class_type.instance_type),
+	('PLANK', PLANK_Class_),#.class_type.instance_type),
+	('PHCARB', PHCARB_Class_),#.class_type.instance_type),
 	('AFACT', nb.float64),
 	('ALK', nb.float64[:]),
 	('AVDEP', nb.float64[:]),

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")