Adding first version of .github directory

Workflows and templeates were added.

.github/CONTRIBUTING.md

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+# How to contribute
+
+We welcome contributions from external contributors, and this document
+describes how to merge code changes into this projectname. 
+
+## Getting Started
+
+* Make sure you have a [GitHub account](https://github.com/signup/free).
+* [Fork](https://help.github.com/articles/fork-a-repo/) this repository on GitHub.
+* On your local machine,
+  [clone](https://help.github.com/articles/cloning-a-repository/) your fork of
+  the repository.
+
+## Making Changes
+
+* Add some really awesome code to your local fork.  It's usually a [good
+  idea](http://blog.jasonmeridth.com/posts/do-not-issue-pull-requests-from-your-master-branch/)
+  to make changes on a
+  [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/)
+  with the branch name relating to the feature you are going to add.
+* When you are ready for others to examine and comment on your new feature,
+  navigate to your fork of projectname on GitHub and open a [pull
+  request](https://help.github.com/articles/using-pull-requests/) (PR). Note that
+  after you launch a PR from one of your fork's branches, all
+  subsequent commits to that branch will be added to the open pull request
+  automatically.  Each commit added to the PR will be validated for
+  mergability, compilation and test suite compliance; the results of these tests
+  will be visible on the PR page.
+* If you're providing a new feature, you must add test cases and documentation.
+* When the code is ready to go, make sure you run the test suite using pytest.
+* When you're ready to be considered for merging, check the "Ready to go"
+  box on the PR page to let the projectname devs know that the changes are complete.
+  The code will not be merged until this box is checked, the continuous
+  integration returns checkmarks,
+  and multiple core developers give "Approved" reviews.
+
+# Additional Resources
+
+* [General GitHub documentation](https://help.github.com/)
+* [PR best practices](http://codeinthehole.com/writing/pull-requests-and-other-good-practices-for-teams-using-github/)
+* [A guide to contributing to software packages](http://www.contribution-guide.org)
+* [Thinkful PR example](http://www.thinkful.com/learn/github-pull-request-tutorial/#Time-to-Submit-Your-First-PR)

.github/PULL_REQUEST_TEMPLATE.md

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+## Description
+Provide a brief description of the PR's purpose here.
+
+## Todos
+Notable points that this PR has either accomplished or will accomplish.
+  - [ ] TODO 1
+
+## Questions
+- [ ] Question1
+
+## Status
+- [ ] Ready to go

.github/workflows/CI.yaml

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+name: CI
+
+on:
+  # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
+  # Existing codes likely still have "master" as the primary branch
+  # Both are tracked here to keep legacy and new codes working
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+  schedule:
+    # Nightly tests run on master by default:
+    #   Scheduled workflows run on the latest commit on the default or base branch.
+    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
+    - cron: "0 0 * * *"
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macOS-latest, ubuntu-latest] # [macOS-latest, ubuntu-latest, windows-latest]
+        python-version: [3.7] # [3.7, 3.8, 3.9]
+
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - name: Additional info about the build
+      shell: bash
+      run: |
+        uname -a
+
+    - name: Symlink gfortran (macOS)
+      if: runner.os == 'macOS'
+      run: |
+        sudo ln -s /usr/local/bin/gfortran-10 /usr/local/bin/gfortran
+        sudo mkdir /usr/local/gfortran
+        sudo ln -s /usr/local/Cellar/gcc@10/*/lib/gcc/10 /usr/local/gfortran/lib
+        gfortran --version
+
+    - name: Checking gfortran version
+      run: |
+        gfortran --version
+
+    # More info on options: https://github.com/conda-incubator/setup-miniconda
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+        environment-file: devtools/conda-envs/test_env.yaml
+
+        #channels: conda-forge,defaults
+
+        activate-environment: test
+        auto-update-conda: false
+        auto-activate-base: false
+        show-channel-urls: true
+
+
+    - name: Install package
+
+      shell: bash -l {0}
+      run: |
+        python setup.py develop
+        conda list
+
+    - name: Checking version
+
+      shell: bash -l {0}
+      run: |
+        echo 'import molsysmt ; print(molsysmt.__version__)' | python
+
+    - name: Run tests
+
+      shell: bash -l {0}
+      run: |
+        pytest -v --cov=molsysmt --cov-report=xml --color=yes molsysmt/tests/
+
+    - name: CodeCov
+      uses: codecov/codecov-action@v1
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}

.github/workflows/build_and_upload_conda_packages.yaml

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+name: Build and upload conda packages
+
+on:
+  release:
+    types: ['released', 'prereleased']
+
+  workflow_dispatch:
+
+jobs:
+  conda_deployment_with_new_tag:
+    name: Conda deployment of package to platform ${{ matrix.platform }} with Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Conda environment creation and activation
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          environment-file: devtools/conda-envs/build_env.yaml
+          auto-activate-base: false
+          auto-update-conda: false
+          show-channel-urls: true
+      - name: Build and upload the conda packages
+        uses: uibcdf/[email protected]
+        with:
+          meta_yaml_dir: devtools/conda-build
+          python-version: ${{ matrix.python-version }}
+          platform_linux-64: true
+          platform_osx-64: true
+          platform_win-64: true
+          user: uibcdf
+          label: auto
+          token: ${{ secrets.ANACONDA_UIBCDF_TOKEN }}
+

.github/workflows/sphinx_docs_to_gh_pages.yaml

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+name: Sphinx docs to gh-pages
+
+on:
+  release:
+    types: ['released']
+
+  workflow_dispatch:
+
+jobs:
+  sphinx_docs_to_gh-pages:
+    runs-on: ubuntu-latest
+    name: Sphinx docs to gh-pages
+    steps:
+
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Additional info about the build
+        shell: bash
+        run: |
+          uname -a
+
+      - name: Make conda environment
+        uses: conda-incubator/setup-miniconda@v2    # https://github.com/conda-incubator/setup-miniconda
+        with:
+          python-version: 3.7
+          environment-file: devtools/conda-envs/docs_env.yaml
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+          activate-environment: test
+
+      - name: Checking gfortran version
+        run: |
+          gfortran --version
+
+      - name: Install package
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        run: |
+           python setup.py develop
+           conda list
+
+      - name: Checking version
+        shell: bash -l {0}
+        run: |
+           echo 'import openpocket; print(openpocket.__version__)' | python
+
+      - name: Running the Sphinx to gh-pages Action
+        uses: uibcdf/[email protected]
+