refactor commands for reuse in test helpers

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

@@ -27,7 +27,7 @@ jobs:
     - name: Install hsp2
       run: |
         # install the hsp2 executable
-        pip install .
+        pip install .[dev]
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

HSP2tools/HSP2_CLI.py

@@ -1,62 +1,11 @@
 import cltoolbox
 
-from HSP2.main import main as hsp2main
-from HSP2tools.readUCI import readUCI
-from HSP2tools.readWDM import readWDM
-from HSP2IO.hdf import HDF5
-from HSP2IO.io import IOManager
-
-
-@cltoolbox.command()
-def run(hdfname, saveall=True, jupyterlab=False):
-    """Run a HSPsquared model.
-
-    Parameters
-    ----------
-    hdfname: str
-        HDF5 (path) filename used for both input and output.
-    saveall: bool
-        [optional] Default is False.
-        Saves all calculated data ignoring SAVE tables.
-    jupyterlab: bool
-        Jupyterlab
-    """
-    hdf5_instance = HDF5(hdfname)
-    io_manager = IOManager(hdf5_instance)
-    hsp2main(io_manager, saveall=saveall, jupyterlab=jupyterlab)
-
-
-@cltoolbox.command()
-def import_uci(ucifile, h5file):
-    """Import UCI and WDM files into HDF5 file.
-
-    Parameters
-    ----------
-    ucifile: str
-        The UCI file to import into HDF file.
-    h5file: str
-        The destination HDF5 file.
-    """
-    readUCI(ucifile, h5file)
-
-    with open(ucifile, "r") as fp:
-        uci = []
-        for line in fp.readlines():
-            if '***' in line[:81]:
-                continue
-            if not line[:81].strip():
-                continue
-            uci.append(line[:81].rstrip())
-
-    files_start = uci.index("FILES")
-    files_end = uci.index("END FILES")
-
-    for nline in uci[files_start: files_end+1]:
-        if (nline[:10].strip())[:3] == "WDM":
-            readWDM(nline[16:].strip(), h5file)
+from HSP2tools.commands import import_uci, run
 
 
 def main():
+    cltoolbox.command(run)
+    cltoolbox.command(import_uci)
     cltoolbox.main()
 
 

HSP2tools/__init__.py

@@ -1,3 +1,5 @@
+from importlib.metadata import version
+
 from HSP2tools.readHBN import readHBN
 from HSP2tools.readUCI import readUCI
 from HSP2tools.readWDM import readWDM
@@ -9,6 +11,4 @@
 from HSP2tools.graph   import HDF5_isconnected, component_list, color_graph
 
 
-
-import HSP2
-__version__ = HSP2.__version__
+__version__ = version('hsp2')

HSP2tools/commands.py

@@ -0,0 +1,59 @@
+from pathlib import Path
+
+from HSP2.main import main
+from HSP2tools.readUCI import readUCI
+from HSP2tools.readWDM import readWDM
+from HSP2IO.hdf import HDF5
+from HSP2IO.io import IOManager
+
+
+def run(h5file, saveall=True, compress=True):
+    """Run a HSPsquared model.
+
+    Parameters
+    ----------
+    h5file: str
+        HDF5 (path) filename used for both input and output.
+    saveall: bool
+        [optional] Default is True.
+        Saves all calculated data ignoring SAVE tables.
+    compression: bool
+        [optional] Default is True.
+        use compression on the save h5 file.
+    """
+    hdf5_instance = HDF5(h5file)
+    io_manager = IOManager(hdf5_instance)
+    main(io_manager, saveall=saveall, jupyterlab=compress)
+
+
+def import_uci(ucifile, h5file):
+    """Import UCI and WDM files into HDF5 file.
+
+    Parameters
+    ----------
+    ucifile: str
+        The UCI file to import into HDF file.
+    h5file: str
+        The destination HDF5 file.
+    """
+
+    readUCI(ucifile, h5file)
+
+    with open(ucifile, "r") as fp:
+        uci = []
+        for line in fp.readlines():
+            if "***" in line[:81]:
+                continue
+            if not line[:81].strip():
+                continue
+            uci.append(line[:81].rstrip())
+
+    files_start = uci.index("FILES")
+    files_end = uci.index("END FILES")
+
+    uci_dir = Path(ucifile).parent
+    for nline in uci[files_start : files_end + 1]:
+        if (nline[:10].strip())[:3] == "WDM":
+            wdmfile = (uci_dir / nline[16:].strip()).resolve()
+            if wdmfile.exists():
+                readWDM(wdmfile, h5file)

tests/test_regression.py

@@ -2,69 +2,12 @@
 
 import pytest
 
-from HSP2.main import main
-from HSP2tools.readUCI import readUCI
-from HSP2tools.readWDM import readWDM
-from HSP2IO import hdf
+from HSP2tools.commands import import_uci, run
 from HSP2tools.HDF5 import HDF5
 
-from HSP2IO.io import IOManager
-
 from .convert.regression_base import RegressTest as RegressTestBase
 
 
-def import_uci(ucifile, h5file):
-    """Import UCI and WDM files into HDF5 file.
-
-    Parameters
-    ----------
-    ucifile: str
-        The UCI file to import into HDF file.
-    h5file: str
-        The destination HDF5 file.
-    """
-
-    readUCI(ucifile, h5file)
-
-    with open(ucifile, "r") as fp:
-        uci = []
-        for line in fp.readlines():
-            if "***" in line[:81]:
-                continue
-            if not line[:81].strip():
-                continue
-            uci.append(line[:81].rstrip())
-
-    files_start = uci.index("FILES")
-    files_end = uci.index("END FILES")
-
-    uci_dir = Path(ucifile).parent
-    for nline in uci[files_start : files_end + 1]:
-        if (nline[:10].strip())[:3] == "WDM":
-            wdmfile = (uci_dir / nline[16:].strip()).resolve()
-            if wdmfile.exists():
-                readWDM(wdmfile, h5file)
-
-
-def run(h5file, saveall=True, compress=True):
-    """Run a HSPsquared model.
-
-    Parameters
-    ----------
-    h5file: str
-        HDF5 (path) filename used for both input and output.
-    saveall: bool
-        [optional] Default is True.
-        Saves all calculated data ignoring SAVE tables.
-    compression: bool
-        [optional] Default is True.
-        use compression on the save h5 file.
-    """
-    hdf5_instance = hdf.HDF5(h5file)
-    io_manager = IOManager(hdf5_instance)
-    main(io_manager, saveall=saveall, jupyterlab=compress)
-
-
 class RegressTest(RegressTestBase):
     def _get_hsp2_data(self, test_root) -> None:
         test_root_hspf = Path(test_root) / "HSPFresults"