build: restructure project with escience center python template

eScience Center python template is used to restructure the project.

.bumpversion.cfg

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+[bumpversion]
+current_version = 0.1.0
+
+[bumpversion:file:nplinker/main.py]
+search = __version__ = "{current_version}"
+replace = __version__ = "{new_version}"
+
+[bumpversion:file:CITATION.cff]
+search = version: "{current_version}"
+replace = version: "{new_version}"

.dockerignore

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+.bumpversion.cfg
+.editorconfig
+.git
+.github
+.gitignore
+.mlc-config.json
+.prospector.yml
+.vscode
+run_nplinker_docker.sh

.editorconfig

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+# EditorConfig is awesome: http://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+charset = utf-8
+
+# 4 space indentation
+[*.{py,java,r,R,sh}]
+indent_style = space
+indent_size = 4
+
+# 2 space indentation
+[*.{js,json,y{a,}ml,html,cwl}]
+indent_style = space
+indent_size = 2
+
+[*.{md,Rmd,rst}]
+trim_trailing_whitespace = false
+indent_style = space
+indent_size = 2

.github/workflows/cffconvert.yml

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+name: cffconvert
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - CITATION.cff
+  pull_request:
+    branches:
+      - main
+    paths:
+      - CITATION.cff
+
+jobs:
+
+  verify:
+    name: "cffconvert"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        name: Check out a copy of the repository
+
+      - uses: citation-file-format/cffconvert-github-action@main
+        name: Check whether the citation metadata from CITATION.cff is equivalent to that in .zenodo.json

.github/workflows/lint.yml

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+name: Check code style
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - '**.py'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - '**.py'
+
+jobs:
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+      - name: Python info
+        shell: bash -l {0}
+        run: |
+          which python3
+          python3 --version
+      - name: Upgrade pip and install dependencies
+        run: |
+          python3 -m pip install --upgrade pip setuptools
+          pip install "prospector[with_pyroma]" isort
+      - name: Check style against standards using prospector
+        run: prospector
+      - name: Check import order
+        run: isort --check-only . --diff

.github/workflows/markdown-link-check.yml

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+name: markdown-link-check
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - '**.md'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - '**.md'
+
+jobs:
+
+  markdown-link-check:
+    name: Check markdown links
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1
+      with:
+        config-file: '.mlc-config.json'

.github/workflows/publish_gh_release.yml

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+name: Draft or publish Github release
+# this action will automatically create a tag for the latest commit
+
+on:
+  workflow_dispatch:
+    inputs:
+      current_version:
+        description: 'Current version'
+        default: '0.0.1'
+        type: string
+        required: true
+      new_version:
+        description: 'New version to release, used for tag name and release title'
+        default: '0.0.1'
+        type: string
+        required: true
+      mode:
+        description: 'Draft or publish Github release'
+        default: "Draft"
+        required: true
+        type: choice
+        options:
+          - draft
+          - publish
+
+env:
+  REPO_NAME: nplinker-webapp
+  CHANGELOG_FILE: CHANGELOG.md
+  RELEASE_NOTES_FILE: release_notes.md
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    if:  ${{ inputs.current_version != inputs.new_version }}
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+    - name: Upgrade pip and install dependencies
+      run: |
+        python3 -m pip install --upgrade pip
+        pip install bump2version
+    - name: Update package version and change log
+      run: |
+        bumpversion --current-version ${{ inputs.current_version }}  --new-version ${{ inputs.new_version }} part
+        docker run --rm -v "$(pwd)":/usr/local/src/your-app \
+          githubchangeloggenerator/github-changelog-generator \
+          -u ${{ github.repository_owner }} \
+          -p $REPO_NAME \
+          --future-release=v${{ inputs.new_version }} \
+          -o $CHANGELOG_FILE \
+          -t ${{ secrets.GITHUB_TOKEN }}
+    - name: Commit and push the changes
+      uses: stefanzweifel/git-auto-commit-action@v4
+      with:
+        commit_message: Update version to ${{ inputs.new_version }}
+    - name: Generate release notes
+      run: |
+        awk '/^## \[v${{ inputs.new_version }}/{flag=1; next}/^##/{flag=0}flag' $CHANGELOG_FILE > $RELEASE_NOTES_FILE
+    - name: Draft a Github release
+      if: ${{ inputs.mode == 'draft' }}
+      run: |
+        gh release create v${{ inputs.new_version }} --draft --title v${{ inputs.new_version }} -F $RELEASE_NOTES_FILE
+      env:
+        GITHUB_TOKEN: ${{ secrets.GH_ACTION_TOKEN }}
+    - name: Publish a Github release
+      if: ${{ inputs.mode == 'publish' }}
+      run: |
+        gh release create v${{ inputs.new_version }} --title v${{ inputs.new_version }} -F $RELEASE_NOTES_FILE
+      env:
+        GITHUB_TOKEN: ${{ secrets.GH_ACTION_TOKEN }}

.gitignore

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+
+*.pyc

.mlc-config.json

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+{
+    "_comment": "Markdown Link Checker configuration, see https://github.com/gaurav-nelson/github-action-markdown-link-check and https://github.com/tcort/markdown-link-check",
+    "ignorePatterns": [
+        {
+            "pattern": "^http://localhost"
+        },
+        {
+          "pattern": "^https://doi.org/<replace-with-created-DOI>"
+        },
+        {
+          "pattern": "^https://github.com/.*/settings/secrets/actions$"
+        },
+        {
+          "pattern": "^https://github.com/organizations/.*/repositories/new"
+        },
+        {
+          "pattern": "^https://help.github.com/.*"
+        },
+        {
+          "pattern": "^https://docs.github.com/.*"
+        },
+        {
+          "pattern": "^https://test.pypi.org"
+        },
+        {
+          "pattern": "^https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>"
+        },
+        {
+          "pattern": "^https://readthedocs.org/dashboard/import.*"
+        }
+    ],
+    "replacementPatterns": [
+    ],
+    "retryOn429": true,
+    "timeout": "20s"
+}

.prospector.yml

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+# prospector configuration file
+
+---
+
+output-format: grouped
+
+strictness: medium
+doc-warnings: false
+test-warnings: true
+member-warnings: false
+
+ignore-paths:
+  - docs
+  - notebooks
+
+pyroma:
+    run: true
+
+pycodestyle:
+    full: true
+
+pydocstyle:
+    disable: [
+        # Disable because not part of PEP257 official convention:
+        # see http://pep257.readthedocs.io/en/latest/error_codes.html
+        D203,  # 1 blank line required before class docstring
+        D212,  # Multi-line docstring summary should start at the first line
+        D213,  # Multi-line docstring summary should start at the second line
+        D404,  # First word of the docstring should not be This
+    ]

.vscode/settings.json

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+{
+  "editor.rulers": [
+    72,
+    79
+  ],
+
+  // python
+  "[python]": {
+    "editor.defaultFormatter": "ms-python.python"
+  },
+  "python.analysis.completeFunctionParens": true,
+  "python.autoComplete.addBrackets": true,
+  "python.defaultInterpreterPath": "",
+  "python.languageServer": "Pylance",
+  // formatting and linting
+  "python.formatting.provider": "yapf",
+  "python.linting.enabled": true,
+  "python.linting.prospectorEnabled": true,
+  "python.linting.pylintEnabled": false,
+  // python docstring
+  "autoDocstring.docstringFormat": "google",
+  "autoDocstring.customTemplatePath": ".vscode/vscode_docstring_google_adapted.mustache",
+
+  // Jupyter
+  "jupyter.sendSelectionToInteractiveWindow": true,
+  "jupyter.askForKernelRestart": false,
+  "notebook.lineNumbers": "on",
+  "notebook.diff.ignoreMetadata": true
+}

.vscode/vscode_docstring_google_adapted.mustache

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+{{! Google Docstring Template}}
+{{summaryPlaceholder}}
+
+{{extendedSummaryPlaceholder}}
+
+{{  # parametersExist}}
+Args:
+{{  # args}}
+    {{var}}({{typePlaceholder}}): {{descriptionPlaceholder}}
+{{/args}}
+{{  # kwargs}}
+    {{var}} ({{typePlaceholder}}, optional): {{descriptionPlaceholder}}. Defaults to {{& default}}.
+{{/kwargs}}
+{{/parametersExist}}
+
+{{  # exceptionsExist}}
+Raises:
+{{  # exceptions}}
+    {{type}}: {{descriptionPlaceholder}}
+{{/exceptions}}
+{{/exceptionsExist}}
+
+{{  # returnsExist}}
+Returns:
+{{  # returns}}
+    {{typePlaceholder}}: {{descriptionPlaceholder}}
+{{/returns}}
+{{/returnsExist}}
+
+Examples:
+    >>> {{#placeholder}}
+    {{/placeholder}}