initial commit

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+ignore = E203, E266, E501, W503, C901, E722, E731, W605, E712, F841, D202, D203
+max-line-length = 88
+max-complexity = 18
+select = B,C,E,F,W,T4

.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+* HapiSM version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/custom.md

@@ -0,0 +1,8 @@
+---
+name: Custom issue template
+about: Describe this issue template's purpose here.
+title: ''
+labels: ''
+assignees: ''
+
+---

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/conda-deployment.yml

@@ -0,0 +1,46 @@
+name: conda-deployment
+
+on: [push]
+
+jobs:
+  Main-package:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.11"]
+    env:
+      OS: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          mamba-version: "*"
+          #use-mamba: true
+          auto-update-conda: false
+          environment-file: environment.yml
+          auto-activate-base: false
+          activate-environment: test
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge,defaults
+          channel-priority: true
+          show-channel-urls: true
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
+
+      - name: Install dev-dependencies
+        run: |
+            python -m pip install -r requirements-dev.txt
+
+      - name: Generate coverage report
+        shell: bash -el {0}
+        run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
+          pytest -sv -m "not plot"

.github/workflows/github-release.yml

@@ -0,0 +1,36 @@
+name: gitHub-release
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - '*'
+
+jobs:
+  create-release:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Setup GitHub CLI
+        run: |
+          type -p curl >/dev/null || (sudo apt update && sudo apt install curl -y)
+          curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | sudo dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg \
+          && sudo chmod go+r /usr/share/keyrings/githubcli-archive-keyring.gpg \
+          && echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | sudo tee /etc/apt/sources.list.d/github-cli.list > /dev/null \
+          && sudo apt update \
+          && sudo apt install gh -y
+
+      - name: Extract tag name
+        run: echo "TAG_NAME=${GITHUB_REF#refs/tags/}" >> $GITHUB_ENV
+
+
+      - name: Create GitHub Release
+        id: create_release
+        run: |
+          gh release create $TAG_NAME --title "$TAG_NAME"  --notes-from-tag
+        env:
+          GH_TOKEN: ${{ secrets.CREATE_RELEASE }}

.github/workflows/pypi-deployment.yml

@@ -0,0 +1,47 @@
+name: pypi-deployment
+
+on: [push]
+
+jobs:
+  Main-Package:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.11", "3.12"]
+    env:
+      OS: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
+
+      - name: Install GDAL
+        run: |
+            python -m pip install --upgrade pip
+            pip install --no-cache-dir Cython
+            pip install --find-links=https://girder.github.io/large_image_wheels --no-cache GDAL #==3.7.1
+
+      - name: Test GDAL installation
+        run: |
+            python -c "from osgeo import gdal"
+            gdalinfo --version
+
+      - name: Install dependencies
+        run: |
+            pip install -r requirements.txt -r requirements-dev.txt
+            python setup.py install
+
+      - name: Generate coverage report
+        run: |
+          conda info
+          conda config --show-sources
+          conda config --show
+          python -m pytest -vvv --cov=serapis --cov-report=xml
+
+      - name: Upload coverage reports to Codecov with GitHub Action
+        uses: codecov/codecov-action@v3

.github/workflows/pypi-release.yml

@@ -0,0 +1,30 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: pypi-release
+
+on:
+    release:
+        types: [created]
+
+jobs:
+    deploy:
+        runs-on: ubuntu-latest
+
+        steps:
+            - uses: actions/checkout@v3
+            - name: Set up Python
+              uses: actions/setup-python@v4
+              with:
+                  python-version: "3.x"
+            - name: Install dependencies
+              run: |
+                  python -m pip install --upgrade pip
+                  pip install setuptools wheel twine
+            - name: Build and publish
+              env:
+                  TWINE_USERNAME: ${{ secrets.PYPI_USERS }}
+                  TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+              run: |
+                  python setup.py sdist bdist_wheel
+                  twine upload dist/*

.gitignore

@@ -157,4 +157,4 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/

.pre-commit-config.yaml

@@ -0,0 +1,114 @@
+fail_fast: true
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: end-of-file-fixer
+        name: "[py -  check] validate yaml"
+      - id: trailing-whitespace
+        name: "[file - format] trim trailing whitespace"
+        args: [ --markdown-linebreak-ext=md ]
+      - id: check-added-large-files
+        name: "[file -  check] large file"
+        args: [ --maxkb=5000 ]
+      - id: check-docstring-first
+        name: "[py   -  check] docstring first"
+        files: /examples
+        types : [file, python ]
+      - id: check-json
+        name: "[json -  check] validate json"
+      - id: check-merge-conflict
+        name: "[git  -  check] merge conflict"
+      - id: debug-statements
+        name: "[py   -  check] debug statements"
+      - id: detect-private-key
+        name: "[cred -  check] private keys"
+      - id: fix-encoding-pragma
+        name: "[file - format] coding pragma"
+        args: [ --remove ]
+      - id: mixed-line-ending
+        name: "[file - format] mixed line ending"
+        args: [ --fix=auto ]
+      - id: pretty-format-json
+        name: "[json - format] pretty json"
+        args: [ --autofix,
+                --indent=4,
+                --no-sort-keys ]
+      - id: requirements-txt-fixer
+        name: "[reqs - format] fix requirements.txt"
+      - id: check-yaml
+        name: "[yaml -  check] validate yaml"
+#  - repo: https://github.com/pre-commit/mirrors-isort
+#    rev: v5.10.1
+#    hooks:
+#      - id: isort
+#        name: "[py   - format] isort"
+#  - repo: https://github.com/PyCQA/docformatter
+#    rev: v1.4
+#    hooks:
+#      - id: docformatter
+#        name: "[py   - format] docformatter"
+#        args: [ -i, --wrap-summaries, "0" ]
+
+  - repo: https://github.com/PyCQA/pydocstyle
+    rev: 6.3.0
+    hooks:
+      - id: pydocstyle
+        name: "[py   - check] pydocstyle"
+        files: ^Hapi/
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+        name: "[py   - check] flake8"
+#        language_version: python3.9
+        exclude: ^(examples/|tests/)
+
+  #- repo: https://github.com/psf/black
+  #  rev: 22.8.0
+  #  hooks:
+  #    - id: black
+  - repo: https://github.com/ambv/black
+    rev: 23.11.0
+    hooks:
+      - id: black
+        name: "[py   - format] black"
+#        language_version: python3.9
+  - repo: https://github.com/lovesegfault/beautysh
+    rev: v6.2.1
+    hooks:
+      - id: beautysh
+        name: "[bash - format] beautysh"
+
+  # pre-commit-shell: Checks shell scripts against shellcheck.
+  - repo: https://github.com/detailyang/pre-commit-shell
+    rev: 1.0.5
+    hooks:
+      - id: shell-lint
+        name: "[bash -   lint] shell-lint"
+
+  - repo: https://github.com/rlindsgaard/pre-commit-commit-msg-hooks
+    rev: 0.1.0
+    hooks:
+      - id: check-description-max-length
+        name: "[bash -   format] check-description-max-length"
+      - id: check-second-line-empty
+        name: "[bash -   format] check-second-line-empty"
+      - id: check-summary-capitalized
+        name: "[bash -   format] check-summary-capitalized"
+      - id: check-summary-imperative
+        name: "[bash -   format] check-summary-imperative"
+      - id: check-summary-max-length
+        name: "[bash -   format] check-summary-max-length"
+      - id: check-summary-punctuation
+        name: "[bash -   format] check-summary-punctuation"
+
+  - repo: local
+    hooks:
+      - id: pytest-check
+        name: pytest-check
+        entry: pytest -vvv --cov=serapis --cov-report term-missing
+        language: system
+        pass_filenames: false
+        always_run: true

.pydocstyle

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+[pydocstyle]
+ignore = D202, D413, D417, D107, D213, D203

.readthedocs.yml

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+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+conda:
+  environment: docs/environment.yml
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+#Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all