move away from poetry, doc improvements, gui fixes

* bokeh 3 fix and bug fix * bumping version requirements * moving load of data and added get_edge * fixes to data * adding tests * added custom material example * added example that show edges * moved api to generated dir and added clean command to make * bug fixes and improvements to gui * Update .gitignore * fixes to docs * update to tests for edges * update to bokeh version pin * expanded get_element_symbol ability and solved issue #52 * removed poetry * Update codestyle.yml * fixes tests and linting * Update testing.yml * Update .pre-commit-config.yaml * added pre-commit checks * Update pyproject.toml * moved precommit to its own workflow * fixed missing doc dependency * pre-commit fixes * not needed because get_atomic_number issue error already * fix for new version of black req * Update README.rst * update to black version req and black fix * fixed license file reference * fixed dynamic version number and cleanup
ehsteve · Mar 12, 2024 · 3f3d2c7 · 3f3d2c7
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diff --git a/.github/workflows/codestyle.yml b/.github/workflows/codestyle.yml
@@ -1,4 +1,4 @@
-# This workflow will install Python dependencies, run tests, run linting, and test building docs
+# This workflow will install Python dependencies and check code style and linting
 name: Codestyle and Linting
 
 on:
@@ -8,42 +8,34 @@ on:
   pull_request:
     branches:
       - main
+
 jobs:
   build:
-    runs-on: ubuntu-latest
-
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: ["ubuntu-latest"]
+        python-version: ["3.10"]
+    defaults:
+      run:
+        shell: bash
+    runs-on: ${{ matrix.platform }}
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.9
-
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-
-      - name: Load cached venv
-        id: cached-pip-wheels
-        uses: actions/cache@v2
-        with:
-          path: ~/.cache
-          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
-
-      - name: Install dependencies
-        run: poetry install --no-interaction --no-root --with dev
-
-      - name: Install library
-        run: poetry install --no-interaction
-
-      - name: Lint with Black
-        run: |
-          poetry run black --check --diff roentgen
-      - name: flake8
-        run: |
-          poetry run flake8 --count roentgen
-      - name: isort
-        run: |
-          poetry run isort roentgen -c
+        - uses: actions/checkout@v2
+        - name: Set up Python ${{ matrix.python-version }}
+          uses: actions/setup-python@v2
+          with:
+            python-version: ${{ matrix.python-version }}
+        - name: Install dependencies
+          run: |
+            pip install pip setuptools wheel --upgrade
+            python -m pip install -e '.[style]'
+        - name: Lint with Black
+          run: |
+            black --check --diff roentgen
+        - name: flake8
+          run: |
+            flake8 --count roentgen
+        - name: isort
+          run: |
+            isort roentgen -c
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -8,37 +8,28 @@ on:
   pull_request:
     branches:
       - main
+
 jobs:
   build:
-    runs-on: ubuntu-latest
-
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: ["ubuntu-latest"]
+        python-version: ["3.10"]
+    defaults:
+      run:
+        shell: bash
+    runs-on: ${{ matrix.platform }}
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.9
-
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-
-      - name: Load cached venv
-        id: cached-pip-wheels
-        uses: actions/cache@v2
-        with:
-          path: ~/.cache
-          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
-
-      - name: Install dependencies
-        run: poetry install --no-interaction --no-root --with docs
-
-      - name: Install library
-        run: poetry install --no-interaction
-
-      - name: Build docs
-        run: |
-          source $VENV
-          sphinx-build docs docs/_build/html -b html
+        - uses: actions/checkout@v2
+        - name: Set up Python ${{ matrix.python-version }}
+          uses: actions/setup-python@v2
+          with:
+            python-version: ${{ matrix.python-version }}
+        - name: Install dependencies
+          run: |
+            pip install pip setuptools wheel --upgrade
+            python -m pip install -e '.[docs]'
+        - name: Build docs
+          run: |
+            sphinx-build docs docs/_build/html -b html
diff --git a/.github/workflows/precommit.yml b/.github/workflows/precommit.yml
@@ -0,0 +1,26 @@
+# This workflow will install Python dependencies and run a few (not all) pre-commit checks
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/action@v3.0.0
+      with:
+        extra_args: check-ast --all-files
+    - uses: pre-commit/action@v3.0.0
+      with:
+        extra_args: trailing-whitespace --all-files
+    - uses: pre-commit/action@v3.0.0
+      with:
+        extra_args: mixed-line-ending --all-files
+    - uses: pre-commit/action@v3.0.0
+      with:
+        extra_args: debug-statements --all-files
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -8,52 +8,32 @@ on:
   pull_request:
     branches:
       - main
-
 jobs:
   build:
     strategy:
+      fail-fast: false
       matrix:
         platform: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: [3.9]
+        python-version: ["3.10", "3.11"]
     defaults:
       run:
         shell: bash
     runs-on: ${{ matrix.platform }}
     steps:
-      - name: Check out repository
-        uses: actions/checkout@v2
-
-      - name: Set up Python ${{ matrix.python-version }}
-        id: setup-python
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-
-      - name: Load cached venv
-        id: cached-pip-wheels
-        uses: actions/cache@v2
-        with:
-          path: ~/.cache
-          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
-
-      - name: Install dependencies
-        run: poetry install --no-interaction --no-root --with dev
-
-      - name: Install library
-        run: poetry install --no-interaction
-
-      - name: Run tests
-        run: |
-          poetry run pytest --cov=./ --cov-report=xml
-
-      - name: Upload coverage reports to Codecov with GitHub Action
-        uses: codecov/codecov-action@v3
-        with:
-          file: ./coverage.xml
-          fail_ci_if_error: true
+        - uses: actions/checkout@v2
+        - name: Set up Python ${{ matrix.python-version }}
+          uses: actions/setup-python@v2
+          with:
+            python-version: ${{ matrix.python-version }}
+        - name: Install dependencies
+          run: |
+            pip install pip setuptools wheel --upgrade
+            python -m pip install -e '.[tests]'
+        - name: Run tests
+          run: |
+            pytest --cov=./ --cov-report=xml
+        - name: Upload coverage reports to Codecov with GitHub Action
+          uses: codecov/codecov-action@v3
+          with:
+            file: ./coverage.xml
+            fail_ci_if_error: true
diff --git a/.gitignore b/.gitignore
@@ -110,15 +110,15 @@ pip-wheel-metadata/**
 *.c
 
 # Other generated files
-*/version.py
+*/_version.py
 */cython_version.py
 htmlcov
 .coverage
 MANIFEST
 .ipynb_checkpoints
 
 # Sphinx
-docs/api
+docs/generated
 docs/_build
 
 # Eclipse editor project files

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -21,28 +21,29 @@ repos:
   # E902 - IOError
   # F822: undefined name in __all__
   # F823: local variable name referenced before assignment
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.7.9
+  - repo: https://github.com/pycqa/flake8
+    rev: 5.0.4
     hooks:
       - id: flake8
-        args: ['--count', '--select', 'E101,W191,W291,W292,W293,W391,E111,E112,E113,E303,E304,E306,E502,E722,E901,E902,F822,F823']
+        args: ['--count', '--select', 'E501, E203']
 
   - repo: https://github.com/psf/black
-    rev: 21.6b0
+    rev: 24.2.0
     hooks:
       - id: black
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.4.0
+    rev: v4.5.0
     hooks:
       - id: check-ast
       - id: check-case-conflict
       - id: trailing-whitespace
         exclude: ".*(.fits|.fts|.fit|.txt)$"
-      - id: check-yaml
+      - id: check-toml
+      - id: detect-private-key
       - id: debug-statements
       - id: check-added-large-files
 #      - id: end-of-file-fixer uncommenting this will break the testing of the cookiecutter template
 #        exclude: ".*(.fits|.fts|.fit|.txt|tca.*)$"
       - id: mixed-line-ending
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*)$"
+        exclude: ".*(.fits|.fts|.fit|.txt|tca.*)$"
diff --git a/README.rst b/README.rst
@@ -79,6 +79,7 @@ It is based on `bokeh <https://docs.bokeh.org/en/stable/>`_. To run it locally u
 
    bokeh serve --show <roengten_directory>/gui
 
+An online version of this tool usually working at `https://roentgen-069cf7954bb2.herokuapp.com/gui <https://roentgen-069cf7954bb2.herokuapp.com/gui>`_.
 
 Data Sources
 ============

diff --git a/docs/Makefile b/docs/Makefile
@@ -14,7 +14,12 @@ help:
 
 .PHONY: help Makefile
 
+clean:
+	rm -rf $(BUILDDIR)
+	rm -rf ./generated
+
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
diff --git a/docs/conf.py b/docs/conf.py
@@ -59,6 +59,9 @@
 # documents. Set to the "smart" one.
 default_role = "obj"
 
+# Set automodapi to generate files inside the generated directory
+automodapi_toctreedirnm = "generated/api"
+
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
@@ -99,10 +102,10 @@
 graphviz_output_format = "svg"
 
 graphviz_dot_args = [
-    '-Nfontsize=10',
-    '-Nfontname=Helvetica Neue, Helvetica, Arial, sans-serif',
-    '-Efontsize=10',
-    '-Efontname=Helvetica Neue, Helvetica, Arial, sans-serif',
-    '-Gfontsize=10',
-    '-Gfontname=Helvetica Neue, Helvetica, Arial, sans-serif'
+    "-Nfontsize=10",
+    "-Nfontname=Helvetica Neue, Helvetica, Arial, sans-serif",
+    "-Efontsize=10",
+    "-Efontname=Helvetica Neue, Helvetica, Arial, sans-serif",
+    "-Gfontsize=10",
+    "-Gfontname=Helvetica Neue, Helvetica, Arial, sans-serif",
 ]
diff --git a/docs/examples/tutorial9.rst b/docs/examples/tutorial9.rst
@@ -0,0 +1,29 @@
+Defining your own custom material
+=================================
+Though the compounds list provided in this package is extensive it may not provide the exact material that you are interested in.
+It easily possible to define your own material if you know it's chemical composition.
+The following example, we investigate the absorption of a Gallium Arsenide (GaAs) detector in the same configuration as that in `G. Lioliou & A.M. Barnett (2016) <https://doi.org/10.1016/j.nima.2016.08.047>`__.
+Compare our plot with their `Figure 1 <https://www.sciencedirect.com/science/article/pii/S016890021630866X#f0005>`__.
+
+.. plot::
+    :include-source:
+
+    import astropy.units as u
+    import numpy as np
+
+    from matplotlib import pyplot as plt
+    from roentgen.absorption import Material
+
+    gaas_deadlayer = Material({'Ga': 0.518, 'As': 0.482},
+                            density=5.32*u.g/u.cm**3, thickness=500*u.nm)
+
+    gaas_detector = Material({'Ga': 0.518, 'As': 0.482},
+                            density=5.32*u.g/u.cm**3, thickness=10000*u.nm)
+    e = np.linspace(1, 30, 1000)*u.keV
+
+    plt.plot(e, gaas_detector.absorption(e) * gaas_deadlayer.transmission(e))
+    plt.xlabel(f'Energy [{e.unit}]')
+    plt.ylabel('Quantum Efficiency')
+    plt.ylim(0.001, 1)
+    plt.yscale('log')
+    plt.show()
diff --git a/docs/examples/tutorial_10.rst b/docs/examples/tutorial_10.rst
@@ -0,0 +1,24 @@
+X-ray Transmission through air at STP
+======================================
+
+.. plot::
+    :include-source:
+
+    import numpy as np
+    from matplotlib import pyplot as plt
+    from astropy import constants as const
+    import astropy.units as u
+
+    from roentgen.absorption import Material
+    from roentgen.util import density_ideal_gas
+
+    air_density = density_ideal_gas(1 * const.atm, 20 * u.Celsius)
+    air = Material('air', 1 * u.m, density=air_density)
+
+    e = np.linspace(1, 30, 1000)*u.keV
+
+    plt.plot(e, air.transmission(e))
+    plt.xlabel(f'Energy [{e.unit}]')
+    plt.ylabel('X-ray Transmission through 1 m of air at STP')
+    plt.ylim(0, 1)
+    plt.show()