BUG Fix install with src layout (#506)

* Remove broken docs/examples/nodal_writer.py symlink Wasn't used in docs as a downloadable file, so I don't think it's necessary * Move serpentTools to src/serpentTools : fix installation Closes #499 * Remove pythonpath hack from jupyter notebook testing
CORE-GATECH-GROUP · Aug 23, 2023 · e2822da · e2822da
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diff --git a/.github/workflows/testing.yaml b/.github/workflows/testing.yaml
@@ -49,7 +49,6 @@ jobs:
         # installing. Should be removed with a src-layout
         # https://github.com/CORE-GATECH-GROUP/serpent-tools/issues/499
         run: |
-          export PYTHONPATH=${GITHUB_WORKSPACE}:${PYTHONPATH}
           cd examples
           jupyter execute *ipynb
 

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,5 +1,3 @@
-include versioneer.py
-include serpentTools/_version.py
-include serpentTools/variables.yaml
-include serpentTools/data/*.m
-include serpentTools/data/*.coe
+include src/serpentTools/variables.yaml
+include src/serpentTools/data/*.m
+include src/serpentTools/data/*.coe
diff --git a/docs/examples/nodal_writer.py b/docs/examples/nodal_writer.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -50,7 +50,7 @@ serpentTools = ["variables.yaml"]
 "serpentTools.data" = ["*.m", "*.coe"]
 
 [tool.setuptools.packages.find]
-where = ["serpentTools"]
+where = ["src"]
 
 # This is okay to be empty, but we need a section here
 # in order to trigger it's usage when setting version data

diff --git a/serpentTools/__init__.py → src/serpentTools/__init__.py b/serpentTools/__init__.py → src/serpentTools/__init__.py
diff --git a/serpentTools/__main__.py → src/serpentTools/__main__.py b/serpentTools/__main__.py → src/serpentTools/__main__.py
diff --git a/serpentTools/data/InnerAssembly_res.m → src/serpentTools/data/InnerAssembly_res.m b/serpentTools/data/InnerAssembly_res.m → src/serpentTools/data/InnerAssembly_res.m
diff --git a/serpentTools/data/__init__.py → src/serpentTools/data/__init__.py b/serpentTools/data/__init__.py → src/serpentTools/data/__init__.py
diff --git a/serpentTools/data/bwr_0_dep.m → src/serpentTools/data/bwr_0_dep.m b/serpentTools/data/bwr_0_dep.m → src/serpentTools/data/bwr_0_dep.m
diff --git a/serpentTools/data/bwr_0_det0.m → src/serpentTools/data/bwr_0_det0.m b/serpentTools/data/bwr_0_det0.m → src/serpentTools/data/bwr_0_det0.m
diff --git a/serpentTools/data/bwr_1_dep.m → src/serpentTools/data/bwr_1_dep.m b/serpentTools/data/bwr_1_dep.m → src/serpentTools/data/bwr_1_dep.m
diff --git a/serpentTools/data/bwr_1_det0.m → src/serpentTools/data/bwr_1_det0.m b/serpentTools/data/bwr_1_det0.m → src/serpentTools/data/bwr_1_det0.m
diff --git a/serpentTools/data/bwr_badInventory_dep.m → src/serpentTools/data/bwr_badInventory_dep.m b/serpentTools/data/bwr_badInventory_dep.m → src/serpentTools/data/bwr_badInventory_dep.m
diff --git a/serpentTools/data/bwr_det0.m → src/serpentTools/data/bwr_det0.m b/serpentTools/data/bwr_det0.m → src/serpentTools/data/bwr_det0.m
diff --git a/serpentTools/data/bwr_his0.m → src/serpentTools/data/bwr_his0.m b/serpentTools/data/bwr_his0.m → src/serpentTools/data/bwr_his0.m
diff --git a/serpentTools/data/bwr_longT_dep.m → src/serpentTools/data/bwr_longT_dep.m b/serpentTools/data/bwr_longT_dep.m → src/serpentTools/data/bwr_longT_dep.m
diff --git a/serpentTools/data/bwr_missingT_dep.m → src/serpentTools/data/bwr_missingT_dep.m b/serpentTools/data/bwr_missingT_dep.m → src/serpentTools/data/bwr_missingT_dep.m
diff --git a/serpentTools/data/bwr_noxy_det0.m → src/serpentTools/data/bwr_noxy_det0.m b/serpentTools/data/bwr_noxy_det0.m → src/serpentTools/data/bwr_noxy_det0.m
diff --git a/serpentTools/data/bwr_sens0.m → src/serpentTools/data/bwr_sens0.m b/serpentTools/data/bwr_sens0.m → src/serpentTools/data/bwr_sens0.m
diff --git a/serpentTools/data/bwr_smallxy_det0.m → src/serpentTools/data/bwr_smallxy_det0.m b/serpentTools/data/bwr_smallxy_det0.m → src/serpentTools/data/bwr_smallxy_det0.m
diff --git a/serpentTools/data/demo.coe → src/serpentTools/data/demo.coe b/serpentTools/data/demo.coe → src/serpentTools/data/demo.coe
diff --git a/serpentTools/data/demo_dep.m → src/serpentTools/data/demo_dep.m b/serpentTools/data/demo_dep.m → src/serpentTools/data/demo_dep.m
diff --git a/serpentTools/data/demo_uncs.coe → src/serpentTools/data/demo_uncs.coe b/serpentTools/data/demo_uncs.coe → src/serpentTools/data/demo_uncs.coe
diff --git a/serpentTools/data/depmtx_ref.m → src/serpentTools/data/depmtx_ref.m b/serpentTools/data/depmtx_ref.m → src/serpentTools/data/depmtx_ref.m
diff --git a/serpentTools/data/flattop_sens.m → src/serpentTools/data/flattop_sens.m b/serpentTools/data/flattop_sens.m → src/serpentTools/data/flattop_sens.m
diff --git a/serpentTools/data/fuelPin_det0.m → src/serpentTools/data/fuelPin_det0.m b/serpentTools/data/fuelPin_det0.m → src/serpentTools/data/fuelPin_det0.m
diff --git a/serpentTools/data/hexplot_det0.m → src/serpentTools/data/hexplot_det0.m b/serpentTools/data/hexplot_det0.m → src/serpentTools/data/hexplot_det0.m
diff --git a/serpentTools/data/plut_xs0.m → src/serpentTools/data/plut_xs0.m b/serpentTools/data/plut_xs0.m → src/serpentTools/data/plut_xs0.m
diff --git a/serpentTools/data/pwr_emptyAttributes_res.m → ...rpentTools/data/pwr_emptyAttributes_res.m b/serpentTools/data/pwr_emptyAttributes_res.m → ...rpentTools/data/pwr_emptyAttributes_res.m
diff --git a/serpentTools/data/pwr_filter_res.m → src/serpentTools/data/pwr_filter_res.m b/serpentTools/data/pwr_filter_res.m → src/serpentTools/data/pwr_filter_res.m
diff --git a/serpentTools/data/pwr_noBU_res.m → src/serpentTools/data/pwr_noBU_res.m b/serpentTools/data/pwr_noBU_res.m → src/serpentTools/data/pwr_noBU_res.m
diff --git a/serpentTools/data/pwr_noUniv_res.m → src/serpentTools/data/pwr_noUniv_res.m b/serpentTools/data/pwr_noUniv_res.m → src/serpentTools/data/pwr_noUniv_res.m
diff --git a/serpentTools/data/pwr_res.m → src/serpentTools/data/pwr_res.m b/serpentTools/data/pwr_res.m → src/serpentTools/data/pwr_res.m
diff --git a/serpentTools/data/radplot_det0.m → src/serpentTools/data/radplot_det0.m b/serpentTools/data/radplot_det0.m → src/serpentTools/data/radplot_det0.m
diff --git a/serpentTools/data/ref_branch.coe → src/serpentTools/data/ref_branch.coe b/serpentTools/data/ref_branch.coe → src/serpentTools/data/ref_branch.coe
diff --git a/serpentTools/data/ref_dep.m → src/serpentTools/data/ref_dep.m b/serpentTools/data/ref_dep.m → src/serpentTools/data/ref_dep.m
diff --git a/serpentTools/data/ref_det0.m → src/serpentTools/data/ref_det0.m b/serpentTools/data/ref_det0.m → src/serpentTools/data/ref_det0.m
diff --git a/serpentTools/data/ref_mdx0.m → src/serpentTools/data/ref_mdx0.m b/serpentTools/data/ref_mdx0.m → src/serpentTools/data/ref_mdx0.m
diff --git a/serpentTools/data/ref_noXS_mdx0.m → src/serpentTools/data/ref_noXS_mdx0.m b/serpentTools/data/ref_noXS_mdx0.m → src/serpentTools/data/ref_noXS_mdx0.m
diff --git a/serpentTools/data/time_det0.m → src/serpentTools/data/time_det0.m b/serpentTools/data/time_det0.m → src/serpentTools/data/time_det0.m
diff --git a/serpentTools/detectors.py → src/serpentTools/detectors.py b/serpentTools/detectors.py → src/serpentTools/detectors.py
diff --git a/serpentTools/engines.py → src/serpentTools/engines.py b/serpentTools/engines.py → src/serpentTools/engines.py
diff --git a/serpentTools/io/__init__.py → src/serpentTools/io/__init__.py b/serpentTools/io/__init__.py → src/serpentTools/io/__init__.py
diff --git a/serpentTools/io/base.py → src/serpentTools/io/base.py b/serpentTools/io/base.py → src/serpentTools/io/base.py
diff --git a/serpentTools/io/hooks.py → src/serpentTools/io/hooks.py b/serpentTools/io/hooks.py → src/serpentTools/io/hooks.py
diff --git a/serpentTools/messages.py → src/serpentTools/messages.py b/serpentTools/messages.py → src/serpentTools/messages.py
diff --git a/serpentTools/objects/__init__.py → src/serpentTools/objects/__init__.py b/serpentTools/objects/__init__.py → src/serpentTools/objects/__init__.py
diff --git a/serpentTools/objects/base.py → src/serpentTools/objects/base.py b/serpentTools/objects/base.py → src/serpentTools/objects/base.py
diff --git a/serpentTools/objects/containers.py → src/serpentTools/objects/containers.py b/serpentTools/objects/containers.py → src/serpentTools/objects/containers.py
diff --git a/serpentTools/objects/detectors.py → src/serpentTools/objects/detectors.py b/serpentTools/objects/detectors.py → src/serpentTools/objects/detectors.py
diff --git a/serpentTools/objects/materials.py → src/serpentTools/objects/materials.py b/serpentTools/objects/materials.py → src/serpentTools/objects/materials.py
diff --git a/serpentTools/objects/xsdata.py → src/serpentTools/objects/xsdata.py b/serpentTools/objects/xsdata.py → src/serpentTools/objects/xsdata.py
diff --git a/serpentTools/parsers/__init__.py → src/serpentTools/parsers/__init__.py b/serpentTools/parsers/__init__.py → src/serpentTools/parsers/__init__.py
diff --git a/serpentTools/parsers/_collections.py → src/serpentTools/parsers/_collections.py b/serpentTools/parsers/_collections.py → src/serpentTools/parsers/_collections.py
diff --git a/serpentTools/parsers/base.py → src/serpentTools/parsers/base.py b/serpentTools/parsers/base.py → src/serpentTools/parsers/base.py
diff --git a/serpentTools/parsers/branching.py → src/serpentTools/parsers/branching.py b/serpentTools/parsers/branching.py → src/serpentTools/parsers/branching.py
diff --git a/serpentTools/parsers/bumat.py → src/serpentTools/parsers/bumat.py b/serpentTools/parsers/bumat.py → src/serpentTools/parsers/bumat.py
diff --git a/serpentTools/parsers/depletion.py → src/serpentTools/parsers/depletion.py b/serpentTools/parsers/depletion.py → src/serpentTools/parsers/depletion.py
diff --git a/serpentTools/parsers/depmatrix.py → src/serpentTools/parsers/depmatrix.py b/serpentTools/parsers/depmatrix.py → src/serpentTools/parsers/depmatrix.py
diff --git a/serpentTools/parsers/detector.py → src/serpentTools/parsers/detector.py b/serpentTools/parsers/detector.py → src/serpentTools/parsers/detector.py
diff --git a/serpentTools/parsers/fissionMatrix.py → src/serpentTools/parsers/fissionMatrix.py b/serpentTools/parsers/fissionMatrix.py → src/serpentTools/parsers/fissionMatrix.py
diff --git a/serpentTools/parsers/history.py → src/serpentTools/parsers/history.py b/serpentTools/parsers/history.py → src/serpentTools/parsers/history.py
diff --git a/serpentTools/parsers/microxs.py → src/serpentTools/parsers/microxs.py b/serpentTools/parsers/microxs.py → src/serpentTools/parsers/microxs.py
diff --git a/serpentTools/parsers/results.py → src/serpentTools/parsers/results.py b/serpentTools/parsers/results.py → src/serpentTools/parsers/results.py
diff --git a/serpentTools/parsers/sensitivity.py → src/serpentTools/parsers/sensitivity.py b/serpentTools/parsers/sensitivity.py → src/serpentTools/parsers/sensitivity.py
diff --git a/serpentTools/parsers/xsplot.py → src/serpentTools/parsers/xsplot.py b/serpentTools/parsers/xsplot.py → src/serpentTools/parsers/xsplot.py
diff --git a/serpentTools/plot.py → src/serpentTools/plot.py b/serpentTools/plot.py → src/serpentTools/plot.py
diff --git a/serpentTools/samplers/__init__.py → src/serpentTools/samplers/__init__.py b/serpentTools/samplers/__init__.py → src/serpentTools/samplers/__init__.py
diff --git a/serpentTools/samplers/base.py → src/serpentTools/samplers/base.py b/serpentTools/samplers/base.py → src/serpentTools/samplers/base.py
diff --git a/serpentTools/samplers/depletion.py → src/serpentTools/samplers/depletion.py b/serpentTools/samplers/depletion.py → src/serpentTools/samplers/depletion.py
diff --git a/serpentTools/samplers/detector.py → src/serpentTools/samplers/detector.py b/serpentTools/samplers/detector.py → src/serpentTools/samplers/detector.py
diff --git a/serpentTools/seed.py → src/serpentTools/seed.py b/serpentTools/seed.py → src/serpentTools/seed.py
diff --git a/serpentTools/settings.py → src/serpentTools/settings.py b/serpentTools/settings.py → src/serpentTools/settings.py
diff --git a/serpentTools/utils/__init__.py → src/serpentTools/utils/__init__.py b/serpentTools/utils/__init__.py → src/serpentTools/utils/__init__.py
diff --git a/serpentTools/utils/compare.py → src/serpentTools/utils/compare.py b/serpentTools/utils/compare.py → src/serpentTools/utils/compare.py
diff --git a/serpentTools/utils/core.py → src/serpentTools/utils/core.py b/serpentTools/utils/core.py → src/serpentTools/utils/core.py
diff --git a/serpentTools/utils/docstrings.py → src/serpentTools/utils/docstrings.py b/serpentTools/utils/docstrings.py → src/serpentTools/utils/docstrings.py
diff --git a/serpentTools/utils/plot.py → src/serpentTools/utils/plot.py b/serpentTools/utils/plot.py → src/serpentTools/utils/plot.py
diff --git a/serpentTools/variables.yaml → src/serpentTools/variables.yaml b/serpentTools/variables.yaml → src/serpentTools/variables.yaml
diff --git a/serpentTools/xs.py → src/serpentTools/xs.py b/serpentTools/xs.py → src/serpentTools/xs.py