Remove check for added large files from pre-commit hooks

NOC-MSM · May 26, 2023 · 2a05838 · 2a05838
1 parent 6016c61
commit 2a05838
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Showing 63 changed files with 44 additions and 183 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,7 +7,6 @@ repos:
   - id: check-json
   - id: check-yaml
   - id: check-toml
-  - id: check-added-large-files
   - id: debug-statements
   - id: mixed-line-ending
 - repo: https://github.com/psf/black

diff --git a/pynemo_37.yml b/pynemo_37.yml
diff --git a/pynemo_39.yml b/pynemo_39.yml
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,24 +1,51 @@
 [build-system]
 requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
 
+[options]
+install_requires = [
+  "netCDF4",
+  "scipy",
+  "numpy",
+  "matplotlib",
+  "basemap",
+  "thredds_crawler",
+  "seawater"
+]
+
 [project]
+authors = [
+  {name = "James Harle", email = "[email protected]"},
+  {name = "John Kazimierz Farey"},
+  {name = "Srikanth Nagella"},
+  {name = "Shirley Crompton"},
+  {name = "Tom Prime"}
+]
 classifiers = [
+  "License :: OSI Approved :: GPL License",
   "Development Status :: 2 - Pre-Alpha",
   "Intended Audience :: Science/Research",
-  "License :: OSI Approved :: Apache Software License",
-  "Operating System :: OS Independent",
+  "Intended Audience :: Developers",
+  "Topic :: Oceonography Modelling",
+  "Topic :: Scientific/Engineering",
   "Programming Language :: Python",
-  "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.10",
-  "Programming Language :: Python :: 3.11",
-  "Topic :: Scientific/Engineering"
+  "Programming Language :: Python :: 3.9"
 ]
-description = "a Python based regional NEMO model configuration toolbox"
+description = "NEMO Regional Configuration Toolbox"
 dynamic = ["version"]
+keywords = ["Oceanography", "NEMO"]
 license = {file = "LICENSE"}
 name = "PyNEMO"
 readme = "README.md"
 
+[project.scripts]
+pynemo = "pynemo.pynemo_exe:main"
+pynemo_ncml_generator = "pynemo.pynemo_ncml_generator:main"
+pynemo_settings_editor = "pynemo.pynemo_settings_editor:main"
+
+[project.urls]
+documentation = "https://pynemo.readthedocs.io/en/latest/"
+repository = "https://github.com/NOC-MSM/PyNEMO"
+
 [tool.coverage.run]
 branch = true
 
@@ -56,11 +83,18 @@ select = [
   "D"
 ]
 
-[tool.setuptools]
-packages = ["pynemo"]
+[tool.setuptools.package-data]
+gui = ["*.png", "*.ncml"]
+"pynemo" = ["*.info"]
+"reader.jars" = ["*.jar"]
+share = ["epsg"]
+
+[tool.setuptools.packages.find]
+namespaces = true
+where = ["src"]
 
 [tool.setuptools_scm]
-write_to = "pynemo/version.py"
+write_to = "src/pynemo/version.py"
 write_to_template = '''
 # Do not change! Do not track in version control!
 __version__ = "{version}"

diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/pynemo/__init__.py → src/pynemo/__init__.py b/pynemo/__init__.py → src/pynemo/__init__.py
diff --git a/pynemo/gui/__init__.py → src/pynemo/gui/__init__.py b/pynemo/gui/__init__.py → src/pynemo/gui/__init__.py
diff --git a/pynemo/gui/all_mask.png → src/pynemo/gui/all_mask.png b/pynemo/gui/all_mask.png → src/pynemo/gui/all_mask.png
diff --git a/pynemo/gui/base.ncml → src/pynemo/gui/base.ncml b/pynemo/gui/base.ncml → src/pynemo/gui/base.ncml
diff --git a/pynemo/gui/border.png → src/pynemo/gui/border.png b/pynemo/gui/border.png → src/pynemo/gui/border.png
diff --git a/pynemo/gui/freehand.png → src/pynemo/gui/freehand.png b/pynemo/gui/freehand.png → src/pynemo/gui/freehand.png
diff --git a/pynemo/gui/max_depth.png → src/pynemo/gui/max_depth.png b/pynemo/gui/max_depth.png → src/pynemo/gui/max_depth.png
diff --git a/pynemo/gui/minus.png → src/pynemo/gui/minus.png b/pynemo/gui/minus.png → src/pynemo/gui/minus.png
diff --git a/pynemo/gui/mynormalize.py → src/pynemo/gui/mynormalize.py b/pynemo/gui/mynormalize.py → src/pynemo/gui/mynormalize.py
diff --git a/pynemo/gui/nemo-icon.png → src/pynemo/gui/nemo-icon.png b/pynemo/gui/nemo-icon.png → src/pynemo/gui/nemo-icon.png
diff --git a/pynemo/gui/nemo_bdy_input_window.py → src/pynemo/gui/nemo_bdy_input_window.py b/pynemo/gui/nemo_bdy_input_window.py → src/pynemo/gui/nemo_bdy_input_window.py
diff --git a/pynemo/gui/nemo_bdy_mask.py → src/pynemo/gui/nemo_bdy_mask.py b/pynemo/gui/nemo_bdy_mask.py → src/pynemo/gui/nemo_bdy_mask.py
diff --git a/pynemo/gui/nemo_bdy_mask_gui.py → src/pynemo/gui/nemo_bdy_mask_gui.py b/pynemo/gui/nemo_bdy_mask_gui.py → src/pynemo/gui/nemo_bdy_mask_gui.py
diff --git a/...gui/nemo_bdy_mask_gui.py.interactive_cbar → ...gui/nemo_bdy_mask_gui.py.interactive_cbar b/...gui/nemo_bdy_mask_gui.py.interactive_cbar → ...gui/nemo_bdy_mask_gui.py.interactive_cbar
diff --git a/pynemo/gui/nemo_bdy_namelist_edit.py → src/pynemo/gui/nemo_bdy_namelist_edit.py b/pynemo/gui/nemo_bdy_namelist_edit.py → src/pynemo/gui/nemo_bdy_namelist_edit.py
diff --git a/pynemo/gui/nemo_ncml_generator.py → src/pynemo/gui/nemo_ncml_generator.py b/pynemo/gui/nemo_ncml_generator.py → src/pynemo/gui/nemo_ncml_generator.py
diff --git a/pynemo/gui/nemo_ncml_tab_widget.py → src/pynemo/gui/nemo_ncml_tab_widget.py b/pynemo/gui/nemo_ncml_tab_widget.py → src/pynemo/gui/nemo_ncml_tab_widget.py
diff --git a/pynemo/gui/plus.png → src/pynemo/gui/plus.png b/pynemo/gui/plus.png → src/pynemo/gui/plus.png
diff --git a/pynemo/gui/rectangle.png → src/pynemo/gui/rectangle.png b/pynemo/gui/rectangle.png → src/pynemo/gui/rectangle.png
diff --git a/pynemo/gui/reset.png → src/pynemo/gui/reset.png b/pynemo/gui/reset.png → src/pynemo/gui/reset.png
diff --git a/pynemo/gui/selection_editor.py → src/pynemo/gui/selection_editor.py b/pynemo/gui/selection_editor.py → src/pynemo/gui/selection_editor.py
diff --git a/pynemo/gui/shelf_break.png → src/pynemo/gui/shelf_break.png b/pynemo/gui/shelf_break.png → src/pynemo/gui/shelf_break.png
diff --git a/pynemo/nemo_bdy_dst_coord.py → src/pynemo/nemo_bdy_dst_coord.py b/pynemo/nemo_bdy_dst_coord.py → src/pynemo/nemo_bdy_dst_coord.py
diff --git a/pynemo/nemo_bdy_extr_tm3.py → src/pynemo/nemo_bdy_extr_tm3.py b/pynemo/nemo_bdy_extr_tm3.py → src/pynemo/nemo_bdy_extr_tm3.py
diff --git a/pynemo/nemo_bdy_gen_c.py → src/pynemo/nemo_bdy_gen_c.py b/pynemo/nemo_bdy_gen_c.py → src/pynemo/nemo_bdy_gen_c.py
diff --git a/pynemo/nemo_bdy_grid_angle.py → src/pynemo/nemo_bdy_grid_angle.py b/pynemo/nemo_bdy_grid_angle.py → src/pynemo/nemo_bdy_grid_angle.py
diff --git a/pynemo/nemo_bdy_ice.py → src/pynemo/nemo_bdy_ice.py b/pynemo/nemo_bdy_ice.py → src/pynemo/nemo_bdy_ice.py
diff --git a/pynemo/nemo_bdy_ncgen.py → src/pynemo/nemo_bdy_ncgen.py b/pynemo/nemo_bdy_ncgen.py → src/pynemo/nemo_bdy_ncgen.py
diff --git a/pynemo/nemo_bdy_ncpop.py → src/pynemo/nemo_bdy_ncpop.py b/pynemo/nemo_bdy_ncpop.py → src/pynemo/nemo_bdy_ncpop.py
diff --git a/pynemo/nemo_bdy_scr_coord.py → src/pynemo/nemo_bdy_scr_coord.py b/pynemo/nemo_bdy_scr_coord.py → src/pynemo/nemo_bdy_scr_coord.py
diff --git a/pynemo/nemo_bdy_setup.py → src/pynemo/nemo_bdy_setup.py b/pynemo/nemo_bdy_setup.py → src/pynemo/nemo_bdy_setup.py
diff --git a/pynemo/nemo_bdy_source_coord.py → src/pynemo/nemo_bdy_source_coord.py b/pynemo/nemo_bdy_source_coord.py → src/pynemo/nemo_bdy_source_coord.py
diff --git a/pynemo/nemo_bdy_src_time.py → src/pynemo/nemo_bdy_src_time.py b/pynemo/nemo_bdy_src_time.py → src/pynemo/nemo_bdy_src_time.py
diff --git a/pynemo/nemo_bdy_zgrv2.py → src/pynemo/nemo_bdy_zgrv2.py b/pynemo/nemo_bdy_zgrv2.py → src/pynemo/nemo_bdy_zgrv2.py
diff --git a/pynemo/nemo_coord_gen_pop.py → src/pynemo/nemo_coord_gen_pop.py b/pynemo/nemo_coord_gen_pop.py → src/pynemo/nemo_coord_gen_pop.py
diff --git a/pynemo/profiler.py → src/pynemo/profiler.py b/pynemo/profiler.py → src/pynemo/profiler.py
diff --git a/pynemo/pynemo_exe.py → src/pynemo/pynemo_exe.py b/pynemo/pynemo_exe.py → src/pynemo/pynemo_exe.py
diff --git a/pynemo/pynemo_ncml_generator.py → src/pynemo/pynemo_ncml_generator.py b/pynemo/pynemo_ncml_generator.py → src/pynemo/pynemo_ncml_generator.py
diff --git a/pynemo/pynemo_settings_editor.py → src/pynemo/pynemo_settings_editor.py b/pynemo/pynemo_settings_editor.py → src/pynemo/pynemo_settings_editor.py
diff --git a/pynemo/reader/__init__.py → src/pynemo/reader/__init__.py b/pynemo/reader/__init__.py → src/pynemo/reader/__init__.py
diff --git a/pynemo/reader/directory.py → src/pynemo/reader/directory.py b/pynemo/reader/directory.py → src/pynemo/reader/directory.py
diff --git a/pynemo/reader/factory.py → src/pynemo/reader/factory.py b/pynemo/reader/factory.py → src/pynemo/reader/factory.py
diff --git a/pynemo/reader/jars/netcdfAll-4.6.jar → src/pynemo/reader/jars/netcdfAll-4.6.jar b/pynemo/reader/jars/netcdfAll-4.6.jar → src/pynemo/reader/jars/netcdfAll-4.6.jar
diff --git a/pynemo/reader/ncml.py → src/pynemo/reader/ncml.py b/pynemo/reader/ncml.py → src/pynemo/reader/ncml.py
diff --git a/pynemo/share/epsg → src/pynemo/share/epsg b/pynemo/share/epsg → src/pynemo/share/epsg
diff --git a/pynemo/tide/__init__.py → src/pynemo/tide/__init__.py b/pynemo/tide/__init__.py → src/pynemo/tide/__init__.py
diff --git a/pynemo/tide/fes2014_extract_HC.py → src/pynemo/tide/fes2014_extract_HC.py b/pynemo/tide/fes2014_extract_HC.py → src/pynemo/tide/fes2014_extract_HC.py
diff --git a/pynemo/tide/nemo_bdy_tide.py → src/pynemo/tide/nemo_bdy_tide.py b/pynemo/tide/nemo_bdy_tide.py → src/pynemo/tide/nemo_bdy_tide.py
diff --git a/pynemo/tide/nemo_bdy_tide3.py → src/pynemo/tide/nemo_bdy_tide3.py b/pynemo/tide/nemo_bdy_tide3.py → src/pynemo/tide/nemo_bdy_tide3.py
diff --git a/pynemo/tide/nemo_bdy_tide_ncgen.py → src/pynemo/tide/nemo_bdy_tide_ncgen.py b/pynemo/tide/nemo_bdy_tide_ncgen.py → src/pynemo/tide/nemo_bdy_tide_ncgen.py
diff --git a/pynemo/tide/tpxo_extract_HC.py → src/pynemo/tide/tpxo_extract_HC.py b/pynemo/tide/tpxo_extract_HC.py → src/pynemo/tide/tpxo_extract_HC.py
diff --git a/pynemo/utils/Constants.py → src/pynemo/utils/Constants.py b/pynemo/utils/Constants.py → src/pynemo/utils/Constants.py
diff --git a/pynemo/utils/__init__.py → src/pynemo/utils/__init__.py b/pynemo/utils/__init__.py → src/pynemo/utils/__init__.py
diff --git a/pynemo/utils/e3_to_depth.py → src/pynemo/utils/e3_to_depth.py b/pynemo/utils/e3_to_depth.py → src/pynemo/utils/e3_to_depth.py
diff --git a/pynemo/utils/gcoms_break_depth.py → src/pynemo/utils/gcoms_break_depth.py b/pynemo/utils/gcoms_break_depth.py → src/pynemo/utils/gcoms_break_depth.py
diff --git a/pynemo/utils/nemo_bdy_lib.py → src/pynemo/utils/nemo_bdy_lib.py b/pynemo/utils/nemo_bdy_lib.py → src/pynemo/utils/nemo_bdy_lib.py
diff --git a/pynemo/variable.info → src/pynemo/variable.info b/pynemo/variable.info → src/pynemo/variable.info