Updated env config files (separated out deps for devs) and added gh a…

…ctions workflow

.github/workflows/build_env_run_tests.yml

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+# Builds the aeon environment, flakes via flake8, tests via pytest, reports
+# test coverage via pytest-cov and codecov, and reports security
+# vulnerabilities via bandit.
+
+name: build_env_run_tests
+on:
+  push:
+    branches: [ main, reorg, jai_dev, config ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:  # Allows running manually from Github's 'Actions' tab
+jobs:
+  build_env_run_tests:
+    name: Build env and run tests on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+      fail-fast: false
+    defaults:
+      run:
+        shell: bash -l {0}  # reset shell for each step
+    steps:
+      - name: checkout repo
+        uses: actions/checkout@v2
+      - name: set up conda env
+        uses: conda-incubator/setup-miniconda@v2  # from github marketplace
+        with:
+          activate-environment: aeon
+          environment-file: ./env_config/env.yml
+          use-mamba: true
+          miniforge-variant: Mambaforge
+      - name: Update conda env with dev reqs
+        run: mamba env update -f ./env_config/env_dev.yml
+      - name: flake
+        run: python -m flake8 .
+      - name: bandit
+        run: python -m bandit . -r -ll
+      - name: pytest
+        run: python -m pytest tests/
+      # Only run coverage report job and upload for ubuntu.
+      - name: generate test coverage report
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          python -m pytest --cov=aeon ./tests/ --cov-report=xml:./tests/test_coverage/test_coverage_report.xml
+          python -m pytest --cov=aeon ./tests/ --cov-report=html:./tests/test_coverage/test_coverage_report_html
+      - name: upload test coverage report to codecov
+        if: matrix.os == 'ubuntu-latest'
+        uses: codecov/codecov-action@v2
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          directory: ./tests/test_coverage/
+          files: test_coverage_report.xml
+          fail_ci_if_error: true
+          verbose: true

env_config/.python-version

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+# For installing aeon env via pyenv and poetry
+3.11

env_config/env.yml

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+# Run e.g. w/mamba: `mamba env create -q -f env.yml`
+
+name: aeon
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python>=3.9, <3.12
+  - pip
+  - blas>=2.0, <3
+  - bottleneck>=1.2.1, <2
+  - dash
+  - dotmap
+  - fastparquet
+  - graphviz
+  - ipykernel
+  - jupyter
+  - jupyterlab
+  - matplotlib
+  - numba>=0.46.0, <1
+  - numexpr>=2.6.8, <3
+  - numpy>=1.21.0, <2
+  - pandas>=1.3
+  - plotly
+  - pyarrow
+  - pydotplus
+  - pymysql
+  - pyyaml
+  - scikit-learn
+  - scipy
+  - seaborn
+  - xarray>=0.12.3, <1
+  - pip:
+      - datajoint>=0.13.6, <1
+      - git+https://github.com/datajoint-company/datajoint-utilities.git
+      - opencv-python

env_config/env_dev.yml

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+# Contains only the dev package requirements.
+# Run e.g. w/mamba: `mamba env create -q -f env.yml -f env_dev.yml`
+
+name: aeon
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - bandit
+  - black
+  - flake8
+  - gh
+  - ipdb
+  - isort
+  - pre-commit 
+  - pydantic 
+  - pytest 
+  - pytest-cov 
+  - sphinx 
+  - tox
+  - pip:
+      - git+https://github.com/Technologicat/pyan.git

env_config/env_gpu.yml

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+# Contains only the gpu package requirements.
+# Run e.g. w/mamba: `mamba env create -q -f env.yml -f env_gpu.yml`
+
+name: aeon_gpu
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - cupy
+  - dask

env_config/requirements.txt

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+# Run with `pip install -r requirements.txt`
+
+python>=3.9, <3.12
+pip
+blas>=1.1, <2
+bottleneck>=1.2.1, <2
+datajoint>=0.13, <1
+git+https://github.com/vathes/datajoint-utilities.git
+dotmap
+dash
+fastparquet
+ipykernel
+jupyter
+jupyterlab
+matplotlib
+numba>=0.46.0, <1
+numexpr>=2.6.8, <3
+numpy>=1.21.0, <2
+opencv-python
+pandas>=1.3
+plotly
+pyarrow
+pydotplus
+pymysql
+python-graphviz
+pyyaml
+scikit-learn
+scipy
+seaborn
+xarray>=0.12.3, <1

env_config/requirements_dev.txt

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+# Run with `pip install -r requirements_dev.txt`
+
+-r requirements.txt
+bandit
+black
+flake8
+gh
+ipdb
+isort
+pre-commit
+git+https://github.com/Technologicat/pyan.git
+pydantic
+pytest
+pytest-cov
+sphinx
+tox