Merge pull request #152 from timcera/pypi_package

(feat) change to a pyproject.toml to publish to pypi

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

@@ -1,5 +1,5 @@
 name: Python conda dev application
-# this is a standard setup copied from 
+# 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:
@@ -22,7 +22,8 @@ jobs:
         python-version: "3.11"
     - name: Install dependencies
       run: |
-        $CONDA/bin/conda env update --file environment_dev.yml --name base
+        $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: |
@@ -34,7 +35,7 @@ jobs:
         $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 
+    - name: Test with pytest
       run: |
         $CONDA/bin/conda install pytest
         $CONDA/bin/pytest tests/ptest/test_sysexit.py

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

@@ -1,5 +1,5 @@
 name: Python dev application
-# this is a standard setup copied from 
+# 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:
@@ -23,19 +23,20 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        pip install build
         pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install mando numba pandas tables
     - name: Install hsp2
       run: |
         # install the hsp2 executable using dev environment
-        sudo pip install -e .[dev]
+        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 
+    - 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)

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

@@ -1,5 +1,5 @@
 name: Python application
-# this is a standard setup copied from 
+# 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:
@@ -16,15 +16,15 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v4
       with:
-        python-version: "3.8"
+        python-version: "3.10"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install mando numba pandas tables
     - name: Install hsp2
       run: |
         # install the hsp2 executable
@@ -35,7 +35,7 @@ jobs:
         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 
+    - name: Test with pytest
       run: |
         pytest tests/ptest/test_sysexit.py
         # add additional test, ex:

HSP2tools/HSP2_CLI.py

@@ -1,4 +1,4 @@
-import mando
+import cltoolbox
 
 from HSP2.main import main as hsp2main
 from HSP2tools.readUCI import readUCI
@@ -7,7 +7,7 @@
 from HSP2IO.io import IOManager
 
 
-@mando.command(doctype="numpy")
+@cltoolbox.command()
 def run(hdfname, saveall=True, jupyterlab=False):
     """Run a HSPsquared model.
 
@@ -26,7 +26,7 @@ def run(hdfname, saveall=True, jupyterlab=False):
     hsp2main(io_manager, saveall=saveall, jupyterlab=jupyterlab)
 
 
-@mando.command(doctype="numpy")
+@cltoolbox.command()
 def import_uci(ucifile, h5file):
     """Import UCI and WDM files into HDF5 file.
 
@@ -57,7 +57,7 @@ def import_uci(ucifile, h5file):
 
 
 def main():
-    mando.main()
+    cltoolbox.main()
 
 
 if __name__ == "__main__":