Merge pull request #7 from fusion-energy/develop

improved setup and conda install

.github/workflows/ci_with_install.yml

@@ -22,9 +22,8 @@ jobs:
 
       - name: install package
         run: |
-          pip install -r requirements-test.txt
           conda install -c conda-forge moab
-          python setup.py install
+          pip install .[tests]
 
       - name: Run test_utils
         run: |

.github/workflows/python-publish.yml

@@ -8,6 +8,8 @@
 name: Upload Python Package
 
 on:
+  # allows us to run workflows manually
+  workflow_dispatch:
   release:
     types: [created]
 
@@ -23,27 +25,16 @@ jobs:
       with:
         python-version: '3.x'
 
-    - name: Autobump version
-      run: |
-        # from refs/tags/v1.2.3 get 1.2.3
-        VERSION=$(echo $GITHUB_REF | sed 's#.*/v##')
-        PLACEHOLDER='version="develop"'
-        VERSION_FILE='setup.py'
-        # Grep checks that the placeholder is in the file. If grep doesn't find
-        # the placeholder then it exits with exit code 1 and github actions fails.
-        grep "$PLACEHOLDER" "$VERSION_FILE"
-        sed -i "s/$PLACEHOLDER/version=\"${VERSION}\"/g" "$VERSION_FILE"
-      shell: bash
-
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install setuptools wheel build twine
 
     - name: Build and publish
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
+        twine check dist/*
         twine upload dist/*

.gitignore

@@ -130,3 +130,6 @@ dmypy.json
 
 # dagmc files
 *.h5m
+
+# version file
+_version.py

build.sh

@@ -0,0 +1,2 @@
+python3 -m pip install --upgrade build
+python3 -m build

conda/meta.yaml

@@ -0,0 +1,47 @@
+{% set name = "stl_to_h5m" %}
+{% set version = "0.0.3" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: {{ version }}
+
+source:
+  path: ..
+
+build:
+  number: 0
+  script: python setup.py install --single-version-externally-managed --record=record.txt
+
+requirements:
+  build:
+    - python {{ python }}
+    - setuptools
+  run:
+    - python
+    - moab
+    - numpy
+
+test:
+  imports:
+    - stl_to_h5m
+  requires:
+    - pytest
+  # source_files:
+  #   - tests/
+  #   - examples/
+  # commands:
+  #   - pytest tests
+
+
+about:
+  home: "https://github.com/fusion-energy/stl_to_h5m"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE.txt
+  doc_url: https://github.com/fusion-energy/stl_to_h5m
+  dev_url: https://github.com/fusion-energy/stl_to_h5m
+  summary: stl_to_h5m - Converts STL files to a DAGMC h5m file using PyMoab
+
+extra:
+  recipe-maintainers:
+    - shimwell

conda_build.sh

@@ -0,0 +1,32 @@
+
+#assumes anaconda-client and conda-build have been installed
+# conda install -y anaconda-client
+# conda install -y conda-build
+# anaconda login
+
+#cleans up files that get uploaded to the anaconda repo if not deleted
+find . -name \*.stl -type f -delete
+
+
+rm -rf /tmp/conda-build
+mkdir -p /tmp/conda-build
+rm -rf /tmp/conda-build
+
+conda-build conda/ -c conda-forge --croot /tmp/conda-build 
+
+# converting using all includes quite a few oxs and linux versions.
+# conda convert /tmp/conda-build/linux-64/*.tar.bz2 --platform all  -o /tmp/conda-build
+
+# option for converting package to specified platforms
+# currently there is no moab conda install on win-64
+platforms=( osx-64 linux-64 )
+find /tmp/conda-build/linux-64/ -name *.tar.bz2 | while read file
+do
+    echo $file
+    for platform in "${platforms[@]}"
+    do
+       conda convert --platform $platform $file  -o /tmp/conda-build/
+    done
+done
+
+anaconda upload -f /tmp/conda-build/*/*.tar.bz2

conda_build_config.yaml

@@ -0,0 +1,7 @@
+python:
+    - 3.10
+    - 3.9
+    - 3.8
+    - 3.7
+moab:
+    - 5.3.1

pyproject.toml

@@ -0,0 +1,10 @@
+[build-system]
+requires = [
+    "setuptools >= 45",
+    "wheel",
+    "setuptools_scm[toml] >= 6.2",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "stl_to_h5m/_version.py"

setup.cfg

@@ -0,0 +1,38 @@
+[metadata]
+name = stl_to_h5m
+author = The stl_to_h5m Development Team
+author_email = mail@jshimwell.com
+description = Converts STL files to a DAGMC h5m file using PyMoab
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/fusion-energy/stl_to_h5m
+license = MIT
+license_file = LICENSE.txt
+classifiers =
+    Natural Language :: English
+    Topic :: Scientific/Engineering
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    License :: OSI Approved :: MIT License
+    Operating System :: OS Independent
+project_urls =
+    Source = https://github.com/fusion-energy/stl_to_h5m
+    Tracker = https://github.com/fusion-energy/stl_to_h5m/issues
+
+[options]
+packages = find:
+python_requires= >=3.6
+install_requires=
+    numpy >= 1.21.1
+    # moab is required as well but installed via conda
+
+[options.extras_require]
+tests = 
+    pytest >= 5.4.3
+    dagmc_h5m_file_inspector
+
+[flake8]
+per-file-ignores = __init__.py:F401

setup.py

@@ -1,40 +1,4 @@
 import setuptools
 
-with open("README.md", "r") as fh:
-    long_description = fh.read()
-
-setuptools.setup(
-    name="stl_to_h5m",
-    version="develop",
-    author="The stl_to_h5m Development Team",
-    author_email="mail@jshimwell.com",
-    description="Converts STL files to a DAGMC h5m file using PyMoab",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    url="https://github.com/fusion-energy/stl_to_h5m",
-    packages=setuptools.find_packages(),
-    package_data={
-        "stl_to_h5m": [
-            "requirements.txt",
-            "README.md",
-            "LICENSE",
-            "tests/*.stl",
-        ]
-    },
-    classifiers=[
-        'Natural Language :: English',
-        'Topic :: Scientific/Engineering',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3.9',
-        'License :: OSI Approved :: MIT License',
-        'Operating System :: OS Independent',
-    ],
-    python_requires='>=3.6',
-    install_requires=[
-        "numpy",
-        # 'pymoab' currently only available via conda-forge
-    ],
-)
+if __name__ == "__main__":
+    setuptools.setup()

stl_to_h5m/core.py

@@ -44,12 +44,8 @@ def stl_to_h5m(
         material_tag = entry[1]
 
         moab_core = _add_stl_to_moab_core(
-            moab_core,
-            surface_id,
-            volume_id,
-            material_tag,
-            moab_tags,
-            stl_filename)
+            moab_core, surface_id, volume_id, material_tag, moab_tags, stl_filename
+        )
         volume_id += 1
         surface_id += 1
 

tests/test_python_api.py

@@ -18,9 +18,7 @@ def test_h5m_file_creation_and_contents(self):
         os.system(f"rm {test_h5m_filename}")
 
         returned_filename = stl_to_h5m(
-            files_with_tags=[
-                ("tests/part2.stl", "mat1")
-            ],
+            files_with_tags=[("tests/part2.stl", "mat1")],
             h5m_filename=test_h5m_filename,
         )
 
@@ -29,8 +27,7 @@ def test_h5m_file_creation_and_contents(self):
         assert test_h5m_filename == returned_filename
         assert di.get_volumes_from_h5m(test_h5m_filename) == [1]
         assert di.get_materials_from_h5m(test_h5m_filename) == ["mat1"]
-        assert di.get_volumes_and_materials_from_h5m(
-            test_h5m_filename) == {1: "mat1"}
+        assert di.get_volumes_and_materials_from_h5m(test_h5m_filename) == {1: "mat1"}
 
     def test_h5m_file_creation_and_contents_in_subfolder(self):
         """Checks that a h5m file is created in a subfolder from a single stl
@@ -40,9 +37,7 @@ def test_h5m_file_creation_and_contents_in_subfolder(self):
         os.system(f"rm {test_h5m_filename}")
 
         returned_filename = stl_to_h5m(
-            files_with_tags=[
-                ("tests/part1.stl", "mat1")
-            ],
+            files_with_tags=[("tests/part1.stl", "mat1")],
             h5m_filename=test_h5m_filename,
         )
 
@@ -51,8 +46,7 @@ def test_h5m_file_creation_and_contents_in_subfolder(self):
         assert test_h5m_filename == returned_filename
         assert di.get_volumes_from_h5m(test_h5m_filename) == [1]
         assert di.get_materials_from_h5m(test_h5m_filename) == ["mat1"]
-        assert di.get_volumes_and_materials_from_h5m(
-            test_h5m_filename) == {1: "mat1"}
+        assert di.get_volumes_and_materials_from_h5m(test_h5m_filename) == {1: "mat1"}
 
     def test_h5m_file_creation_and_contents_from_multiple_h5m_files(self):
         """Checks that a h5m file is created from multiple stl files"""
@@ -61,10 +55,7 @@ def test_h5m_file_creation_and_contents_from_multiple_h5m_files(self):
         os.system(f"rm {test_h5m_filename}")
 
         returned_filename = stl_to_h5m(
-            files_with_tags=[
-                ("tests/part1.stl", "mat1"),
-                ("tests/part2.stl", "mat2")
-            ],
+            files_with_tags=[("tests/part1.stl", "mat1"), ("tests/part2.stl", "mat2")],
             h5m_filename=test_h5m_filename,
         )