Development

.bumpversion.cfg

@@ -0,0 +1,32 @@
+[bumpversion]
+current_version = 0.0.5
+commit = True
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
+serialize = 
+	{major}.{minor}.{patch}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+
+[bumpversion:part:build]
+
+[bumpversion:file:./alphabase/__init__.py]
+
+[bumpversion:file:./settings.ini]
+
+[bumpversion:file:./release/one_click_linux_gui/control]
+
+[bumpversion:file:./release/one_click_linux_gui/create_installer_linux.sh]
+
+[bumpversion:file:./release/one_click_macos_gui/distribution.xml]
+
+[bumpversion:file:./release/one_click_macos_gui/Info.plist]
+
+[bumpversion:file:./release/one_click_macos_gui/create_installer_macos.sh]
+
+[bumpversion:file:./release/one_click_windows_gui/create_installer_windows.sh]
+
+[bumpversion:file:./release/one_click_windows_gui/alphabase_innoinstaller.iss]
+search = {current_version}
+replace = {new_version}

.devcontainer.json

@@ -0,0 +1,13 @@
+{
+    "name": "nbdev_template-codespaces",
+    "dockerComposeFile": "docker-compose.yml",
+    "service": "watcher",
+    "settings": {"terminal.integrated.shell.linux": "/bin/bash"},
+    "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind" ],
+    "forwardPorts": [4000, 8080],
+    "appPort": [4000, 8080],
+    "extensions": ["ms-python.python",
+                   "ms-azuretools.vscode-docker"],
+    "runServices": ["notebook", "jekyll", "watcher"],
+    "postStartCommand": "pip install -e ."
+}

.gitattributes

@@ -0,0 +1,2 @@
+**/*.ipynb filter=clean-nbs
+**/*.ipynb diff=ipynb

.gitconfig

@@ -0,0 +1,16 @@
+# Generated by nbdev_install_git_hooks
+#
+# If you need to disable this instrumentation do:
+#   git config --local --unset include.path
+#
+# To restore the filter
+#   git config --local include.path .gitconfig
+#
+# If you see notebooks not stripped, checked the filters are applied in .gitattributes
+#
+[filter "clean-nbs"]
+        clean = nbdev_clean_nbs --read_input_stream True
+        smudge = cat
+        required = true
+[diff "ipynb"]
+        textconv = nbdev_clean_nbs --disp True --fname

.github/workflows/publish_and_release.yml

@@ -25,124 +25,126 @@ jobs:
           cd misc
           . ./check_version.sh
           echo ::set-output name=version::$current_version
-  Create_Draft_On_GitHub:
-    runs-on: ubuntu-latest
-    needs: Version_Bumped
-    outputs:
-      upload_url: ${{ steps.draft_release.outputs.upload_url }}
-    steps:
-      - name: Draft Release
-        id: draft_release
-        uses: actions/create-release@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
-        with:
-          tag_name: ${{ needs.Version_Bumped.outputs.version }}
-          release_name: Release version ${{ needs.Version_Bumped.outputs.version }}
-          draft: false
-          prerelease: false
-  Create_Linux_Release:
-    runs-on: ubuntu-latest
-    needs: Create_Draft_On_GitHub
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-      - name: Conda info
-        shell: bash -l {0}
-        run: conda info
-      - name: Creating installer for Linux
-        shell: bash -l {0}
-        run: |
-          cd release/one_click_linux_gui
-          . ./create_installer_linux.sh
-      - name: Test installer for Linux
-        shell: bash -l {0}
-        run: |
-          sudo dpkg -i release/one_click_linux_gui/dist/AlphaBase_gui_installer_linux.deb
-      - name: Upload Linux Installer
-        id: upload-release-asset
-        uses: actions/upload-release-asset@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: release/one_click_linux_gui/dist/AlphaBase_gui_installer_linux.deb
-          asset_name: AlphaBase_gui_installer_linux.deb
-          asset_content_type: application/octet-stream
-  Create_MacOS_Release:
-    runs-on: macos-latest
-    needs: Create_Draft_On_GitHub
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-      - name: Conda info
-        shell: bash -l {0}
-        run: conda info
-      - name: Creating installer for MacOS
-        shell: bash -l {0}
-        run: |
-          cd release/one_click_macos_gui
-          . ./create_installer_macos.sh
-      - name: Test installer for MacOS
-        shell: bash -l {0}
-        run: |
-          sudo installer -pkg release/one_click_macos_gui/dist/AlphaBase_gui_installer_macos.pkg -target /
-      - name: Upload MacOS Installer
-        id: upload-release-asset
-        uses: actions/upload-release-asset@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: release/one_click_macos_gui/dist/AlphaBase_gui_installer_macos.pkg
-          asset_name: AlphaBase_gui_installer_macos.pkg
-          asset_content_type: application/octet-stream
-  Create_Windows_Release:
-    runs-on: windows-latest
-    needs: Create_Draft_On_GitHub
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-      - name: Conda info
-        shell: bash -l {0}
-        run: conda info
-      - name: Creating installer for Windows
-        shell: bash -l {0}
-        run: |
-          cd release/one_click_windows_gui
-          . ./create_installer_windows.sh
-      - name: Test installer for Windows
-        shell: bash -l {0}
-        run: |
-          cd release/one_click_windows_gui/dist/
-          echo "TODO, this test seems to freeze the runner..."
-          # ./AlphaBase_gui_installer_windows.exe //verysilent //log=log.txt //noicons //tasks= //portable=1
-          # cat log.txt
-      - name: Upload Windows Installer
-        id: upload-release-asset
-        uses: actions/upload-release-asset@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: release/one_click_windows_gui/dist/AlphaBase_gui_installer_windows.exe
-          asset_name: AlphaBase_gui_installer_windows.exe
-          asset_content_type: application/octet-stream
+  # Create_Draft_On_GitHub:
+  #   runs-on: ubuntu-latest
+  #   needs: Version_Bumped
+  #   outputs:
+  #     upload_url: ${{ steps.draft_release.outputs.upload_url }}
+  #   steps:
+  #     - name: Draft Release
+  #       id: draft_release
+  #       uses: actions/create-release@v1
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
+  #       with:
+  #         tag_name: ${{ needs.Version_Bumped.outputs.version }}
+  #         release_name: Release version ${{ needs.Version_Bumped.outputs.version }}
+  #         draft: false
+  #         prerelease: false
+
+
+  # Create_Linux_Release:
+  #   runs-on: ubuntu-latest
+  #   needs: Create_Draft_On_GitHub
+  #   steps:
+  #     - name: Checkout code
+  #       uses: actions/checkout@v2
+  #     - uses: conda-incubator/setup-miniconda@v2
+  #       with:
+  #         auto-update-conda: true
+  #         python-version: ${{ matrix.python-version }}
+  #     - name: Conda info
+  #       shell: bash -l {0}
+  #       run: conda info
+  #     - name: Creating installer for Linux
+  #       shell: bash -l {0}
+  #       run: |
+  #         cd release/one_click_linux_gui
+  #         . ./create_installer_linux.sh
+  #     - name: Test installer for Linux
+  #       shell: bash -l {0}
+  #       run: |
+  #         sudo dpkg -i release/one_click_linux_gui/dist/AlphaBase_gui_installer_linux.deb
+  #     - name: Upload Linux Installer
+  #       id: upload-release-asset
+  #       uses: actions/upload-release-asset@v1
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  #       with:
+  #         upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
+  #         asset_path: release/one_click_linux_gui/dist/AlphaBase_gui_installer_linux.deb
+  #         asset_name: AlphaBase_gui_installer_linux.deb
+  #         asset_content_type: application/octet-stream
+  # Create_MacOS_Release:
+  #   runs-on: macos-latest
+  #   needs: Create_Draft_On_GitHub
+  #   steps:
+  #     - name: Checkout code
+  #       uses: actions/checkout@v2
+  #     - uses: conda-incubator/setup-miniconda@v2
+  #       with:
+  #         auto-update-conda: true
+  #         python-version: ${{ matrix.python-version }}
+  #     - name: Conda info
+  #       shell: bash -l {0}
+  #       run: conda info
+  #     - name: Creating installer for MacOS
+  #       shell: bash -l {0}
+  #       run: |
+  #         cd release/one_click_macos_gui
+  #         . ./create_installer_macos.sh
+  #     - name: Test installer for MacOS
+  #       shell: bash -l {0}
+  #       run: |
+  #         sudo installer -pkg release/one_click_macos_gui/dist/AlphaBase_gui_installer_macos.pkg -target /
+  #     - name: Upload MacOS Installer
+  #       id: upload-release-asset
+  #       uses: actions/upload-release-asset@v1
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  #       with:
+  #         upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
+  #         asset_path: release/one_click_macos_gui/dist/AlphaBase_gui_installer_macos.pkg
+  #         asset_name: AlphaBase_gui_installer_macos.pkg
+  #         asset_content_type: application/octet-stream
+  # Create_Windows_Release:
+  #   runs-on: windows-latest
+  #   needs: Create_Draft_On_GitHub
+  #   steps:
+  #     - name: Checkout code
+  #       uses: actions/checkout@v2
+  #     - uses: conda-incubator/setup-miniconda@v2
+  #       with:
+  #         auto-update-conda: true
+  #         python-version: ${{ matrix.python-version }}
+  #     - name: Conda info
+  #       shell: bash -l {0}
+  #       run: conda info
+  #     - name: Creating installer for Windows
+  #       shell: bash -l {0}
+  #       run: |
+  #         cd release/one_click_windows_gui
+  #         . ./create_installer_windows.sh
+  #     - name: Test installer for Windows
+  #       shell: bash -l {0}
+  #       run: |
+  #         cd release/one_click_windows_gui/dist/
+  #         echo "TODO, this test seems to freeze the runner..."
+  #         # ./AlphaBase_gui_installer_windows.exe //verysilent //log=log.txt //noicons //tasks= //portable=1
+  #         # cat log.txt
+  #     - name: Upload Windows Installer
+  #       id: upload-release-asset
+  #       uses: actions/upload-release-asset@v1
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  #       with:
+  #         upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
+  #         asset_path: release/one_click_windows_gui/dist/AlphaBase_gui_installer_windows.exe
+  #         asset_name: AlphaBase_gui_installer_windows.exe
+  #         asset_content_type: application/octet-stream
   Create_PyPi_Release:
     runs-on: ubuntu-latest
-    needs: [Create_Linux_Release, Create_MacOs_Release, Create_Windows_Release]
+    needs: Version_Bumped
     steps:
       - name: Checkout code
         uses: actions/checkout@v2
@@ -161,7 +163,7 @@ jobs:
       - name: Publish distribution to Test PyPI
         uses: pypa/gh-action-pypi-publish@master
         with:
-          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          password: ${{ secrets.TEST_PYPI_ALPHABASE_API_TOKEN }}
           repository_url: https://test.pypi.org/legacy/
       - name: Test PyPI test release
         shell: bash -l {0}
@@ -171,7 +173,7 @@ jobs:
       - name: Publish distribution to PyPI
         uses: pypa/gh-action-pypi-publish@master
         with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
+          password: ${{ secrets.PYPI_ALPHABASE_API_TOKEN }}
   Test_PyPi_Release:
     name: Test_PyPi_version_on_${{ matrix.os }}
     runs-on: ${{ matrix.os }}

.gitignore

@@ -132,3 +132,6 @@ dmypy.json
 alphabase/logs
 *.DS_Store
 *sandbox*
+
+# vscode temp file
+**/.last_checked

CONTRIBUTING.md

@@ -0,0 +1,33 @@
+# How to contribute
+
+## How to get started
+
+Before anything else, please install the git hooks that run automatic scripts during each commit and merge to strip the notebooks of superfluous metadata (and avoid merge conflicts). After cloning the repository, run the following command inside it:
+```
+nbdev_install_git_hooks
+```
+
+## Did you find a bug?
+
+* Ensure the bug was not already reported by searching on GitHub under Issues.
+* If you're unable to find an open issue addressing the problem, open a new one. Be sure to include a title and clear description, as much relevant information as possible, and a code sample or an executable test case demonstrating the expected behavior that is not occurring.
+* Be sure to add the complete error messages.
+
+#### Did you write a patch that fixes a bug?
+
+* Open a new GitHub pull request with the patch.
+* Ensure that your PR includes a test that fails without your patch, and pass with it.
+* Ensure the PR description clearly describes the problem and solution. Include the relevant issue number if applicable.
+
+## PR submission guidelines
+
+* Keep each PR focused. While it's more convenient, do not combine several unrelated fixes together. Create as many branches as needing to keep each PR focused.
+* Do not mix style changes/fixes with "functional" changes. It's very difficult to review such PRs and it most likely get rejected.
+* Do not add/remove vertical whitespace. Preserve the original style of the file you edit as much as you can.
+* Do not turn an already submitted PR into your development playground. If after you submitted PR, you discovered that more work is needed - close the PR, do the required work and then submit a new PR. Otherwise each of your commits requires attention from maintainers of the project.
+* If, however, you submitted a PR and received a request for changes, you should proceed with commits inside that PR, so that the maintainer can see the incremental fixes and won't need to review the whole PR again. In the exception case where you realize it'll take many many commits to complete the requests, then it's probably best to close the PR, do the work and then submit it again. Use common sense where you'd choose one way over another.
+
+## Do you want to contribute to the documentation?
+
+* Docs are automatically created from the notebooks in the nbs folder.
+