Clean up wheel contents.

Fixes #143. Replaces `setuptools`, which seems very happy to just add everything in the current directory into the source distribution with `hatch`, which is much, much, much more reasonable. Also: * Delete now obsolete `MANIFEST.in` * Delete outdated, non-functional `_debug.py` * Move `init.py` into `neurodamus/data` to properly compartmentalize it SPACK_BRANCH=clean-pydamus SPACK_DEPLOYMENT_SUFFIX=pulls/2358
BlueBrain · Mar 20, 2024 · fb9d035 · fb9d035
1 parent b978f40
commit fb9d035
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Showing 28 changed files with 26 additions and 29 deletions.
diff --git a/.github/workflows/simulation_test.yml b/.github/workflows/simulation_test.yml
@@ -87,19 +87,19 @@ jobs:
         wget --output-document="O1_mods.xz" --quiet "https://zenodo.org/record/8026353/files/O1_mods.xz?download=1"
         tar -xf O1_mods.xz
         cp -r mod tests/share/
-        cp core/mod/*.mod tests/share/mod/
+        cp neurodamus/data/mod/*.mod tests/share/mod/
         ./docker/build_neurodamus.sh tests/share/mod
 
     - name: Example run
       run: |
         export PYTHONPATH=$(pwd)/nrn/build/lib/python:$PYTHONPATH
-        cp core/hoc/* tests/share/hoc/
+        cp neurodamus/data/hoc/* tests/share/hoc/
         export HOC_LIBRARY_PATH=$(pwd)/tests/share/hoc
         # launch simulation with NEURON
-        mpirun -np 2 ./x86_64/special -mpi -python init.py --configFile=tests/simulations/usecase3/simulation_sonata.json
+        mpirun -np 2 ./x86_64/special -mpi -python neurodamus/data/init.py --configFile=tests/simulations/usecase3/simulation_sonata.json
         ls tests/simulations/usecase3/reporting/*.h5
         # launch simulation with CORENEURON
-        mpirun -np 2 ./x86_64/special -mpi -python init.py --configFile=tests/simulations/usecase3/simulation_sonata_coreneuron.json
+        mpirun -np 2 ./x86_64/special -mpi -python neurodamus/data/init.py --configFile=tests/simulations/usecase3/simulation_sonata_coreneuron.json
         ls tests/simulations/usecase3/reporting_coreneuron/*.h5
 
     # - name: live debug session, comment out

diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/_debug.py b/_debug.py
diff --git a/ci/build_ndcore.sh b/ci/build_ndcore.sh
@@ -31,3 +31,7 @@ mkdir -p _lib
 cp -f x86_64/libnrnmech* _lib/
 cp -f $CORE_DIR/hoc/*.hoc _lib/
 cp -f $COMMON_DIR/hoc/*.hoc _lib/
+
+echo $1
+ls -l
+ls -l _lib
diff --git a/neurodamus/core/_neuron.py b/neurodamus/core/_neuron.py
@@ -4,6 +4,7 @@
 """
 from __future__ import absolute_import
 import logging
+import os  # os.environ
 import os.path
 from contextlib import contextmanager
 from .configuration import NeuronStdrunDefaults
@@ -60,8 +61,8 @@ def load_hoc(cls, mod_name):
         h = (cls._h or cls._init())
         mod_filename = mod_name + ".hoc"
         if not h.load_file(mod_filename):
-            raise RuntimeError("Cant load HOC library {}. Consider checking HOC_LIBRARY_PATH"
-                               .format(mod_filename))
+            raise RuntimeError("Cant load HOC library {}. Consider checking HOC_LIBRARY_PATH (currently '{}')"
+                               .format(mod_filename, os.environ.get("HOC_LIBRARY_PATH")))
         cls._hocs_loaded.add(mod_name)
 
     @classmethod

diff --git a/core/hoc/Cell.hoc → neurodamus/data/hoc/Cell.hoc b/core/hoc/Cell.hoc → neurodamus/data/hoc/Cell.hoc
diff --git a/core/hoc/ConnectionUtils.hoc → neurodamus/data/hoc/ConnectionUtils.hoc b/core/hoc/ConnectionUtils.hoc → neurodamus/data/hoc/ConnectionUtils.hoc
diff --git a/core/hoc/Map.hoc → neurodamus/data/hoc/Map.hoc b/core/hoc/Map.hoc → neurodamus/data/hoc/Map.hoc
diff --git a/core/hoc/MorphIO.hoc → neurodamus/data/hoc/MorphIO.hoc b/core/hoc/MorphIO.hoc → neurodamus/data/hoc/MorphIO.hoc
diff --git a/core/hoc/RNGSettings.hoc → neurodamus/data/hoc/RNGSettings.hoc b/core/hoc/RNGSettings.hoc → neurodamus/data/hoc/RNGSettings.hoc
diff --git a/core/hoc/Report.hoc → neurodamus/data/hoc/Report.hoc b/core/hoc/Report.hoc → neurodamus/data/hoc/Report.hoc
diff --git a/core/hoc/TPointList.hoc → neurodamus/data/hoc/TPointList.hoc b/core/hoc/TPointList.hoc → neurodamus/data/hoc/TPointList.hoc
diff --git a/core/hoc/TType.hoc → neurodamus/data/hoc/TType.hoc b/core/hoc/TType.hoc → neurodamus/data/hoc/TType.hoc
diff --git a/core/hoc/defvar.hoc → neurodamus/data/hoc/defvar.hoc b/core/hoc/defvar.hoc → neurodamus/data/hoc/defvar.hoc
diff --git a/core/hoc/fileUtils.hoc → neurodamus/data/hoc/fileUtils.hoc b/core/hoc/fileUtils.hoc → neurodamus/data/hoc/fileUtils.hoc
diff --git a/core/hoc/neurodamus.hoc → neurodamus/data/hoc/neurodamus.hoc b/core/hoc/neurodamus.hoc → neurodamus/data/hoc/neurodamus.hoc
diff --git a/init.py → neurodamus/data/init.py b/init.py → neurodamus/data/init.py
diff --git a/core/mod/ALU.mod → neurodamus/data/mod/ALU.mod b/core/mod/ALU.mod → neurodamus/data/mod/ALU.mod
diff --git a/core/mod/CoreNEURONArtificialCell.mod → ...mus/data/mod/CoreNEURONArtificialCell.mod b/core/mod/CoreNEURONArtificialCell.mod → ...mus/data/mod/CoreNEURONArtificialCell.mod
diff --git a/core/mod/HDF5reader.mod → neurodamus/data/mod/HDF5reader.mod b/core/mod/HDF5reader.mod → neurodamus/data/mod/HDF5reader.mod
diff --git a/core/mod/SonataReportHelper.mod → neurodamus/data/mod/SonataReportHelper.mod b/core/mod/SonataReportHelper.mod → neurodamus/data/mod/SonataReportHelper.mod
diff --git a/core/mod/SonataReports.mod → neurodamus/data/mod/SonataReports.mod b/core/mod/SonataReports.mod → neurodamus/data/mod/SonataReports.mod
diff --git a/core/mod/VecStim.mod → neurodamus/data/mod/VecStim.mod b/core/mod/VecStim.mod → neurodamus/data/mod/VecStim.mod
diff --git a/core/mod/coreneuron_modlist.txt → neurodamus/data/mod/coreneuron_modlist.txt b/core/mod/coreneuron_modlist.txt → neurodamus/data/mod/coreneuron_modlist.txt
diff --git a/core/mod/netstim_inhpoisson.mod → neurodamus/data/mod/netstim_inhpoisson.mod b/core/mod/netstim_inhpoisson.mod → neurodamus/data/mod/netstim_inhpoisson.mod
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,10 +1,9 @@
 [build-system]
 requires = [
-    "setuptools",
-    "setuptools_scm",
-    "wheel"
-    ]
-build-backend = "setuptools.build_meta"
+    "hatchling",
+    "hatch-vcs",
+]
+build-backend = "hatchling.build"
 
 [project]
 name="neurodamus"
@@ -36,10 +35,15 @@ Homepage = "https://github.com/BlueBrain/neurodamus"
 Repository = "https://github.com/BlueBrain/neurodamus.git"
 Tracker = "https://github.com/BlueBrain/neurodamus/issues"
 
-[tool.setuptools.packages.find]
-exclude=["tests"]
+[tool.hatch.build.targets.sdist]
+only-include = [
+    "neurodamus",
+]
+
+[tool.hatch.version]
+source = "vcs"
 
-[tool.setuptools_scm]
+[tool.hatch.version.raw-options]
 local_scheme = "no-local-version"
 
 [tool.pytest.ini_options]

diff --git a/tests/integration/test_cell.py b/tests/integration/test_cell.py
@@ -10,12 +10,12 @@
 
 @pytest.fixture(scope="session")
 def morphologies_root(rootdir):
-    return Path(rootdir) / "tests/sample_data/morphology"
+    return Path(rootdir) / "tests" / "sample_data" / "morphology"
 
 
 @pytest.fixture
 def Cell(rootdir):
-    os.environ["HOC_LIBRARY_PATH"] = str(rootdir) + "/core/hoc"
+    os.environ.setdefault("HOC_LIBRARY_PATH", str(rootdir / "neurodamus" / "data" / "hoc"))
     from neurodamus.core import Cell
     return Cell
 

diff --git a/tox.ini b/tox.ini
@@ -29,7 +29,7 @@ setenv =
 allowlist_externals =
     {toxinidir}/ci/build_ndcore.sh
 commands =
-    {toxinidir}/ci/build_ndcore.sh {toxinidir}/core
+    {toxinidir}/ci/build_ndcore.sh {toxinidir}/neurodamus/data
     pytest -x --forked tests/integration