Merge pull request #76 from ammarcsj/develop_w_loose_install

Merge development branch and improve dependency management

.github/workflows/github_draft_release.yml

@@ -0,0 +1,114 @@
+name: Create GitHub Draft Releases
+
+on:
+  workflow_dispatch:
+
+jobs:
+  Current_Version:
+    runs-on: ubuntu-latest
+    outputs:
+      version: ${{ steps.master_Current_Version.outputs.version }}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - name: Get current version
+        id: master_Current_Version
+        run: |
+          current_version=$(grep "__version__" alphamap/__init__.py | cut -f3 -d ' ' | sed 's/"//g')
+          echo "version=$current_version" >> $GITHUB_OUTPUT
+
+  Create_Draft_On_GitHub:
+    runs-on: ubuntu-latest
+    needs: Current_Version
+    outputs:
+      upload_url: ${{ steps.draft_release.outputs.upload_url }}
+    steps:
+      - name: Create Draft Release
+        id: draft_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: v${{ needs.Current_Version.outputs.version }}
+          release_name: Release version ${{ needs.Current_Version.outputs.version }}
+          draft: true
+          prerelease: false
+      - name: Move release to hidden folder
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          release_id=$(curl -s -H "Authorization: token $GITHUB_TOKEN" \
+            "https://api.github.com/repos/${{ github.repository }}/releases/tags/v${{ needs.Current_Version.outputs.version }}" \
+            | jq -r .id)
+          curl -X PATCH -H "Authorization: token $GITHUB_TOKEN" \
+            -H "Accept: application/vnd.github.v3+json" \
+            "https://api.github.com/repos/${{ github.repository }}/releases/$release_id" \
+            -d '{"draft": true, "name": ".hidden/v${{ needs.Current_Version.outputs.version }}"}'
+  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 }}
+          miniconda-version: "latest"
+      - name: Conda info
+        shell: bash -l {0}
+        run: conda info
+      - name: Creating installer for MacOS
+        shell: bash -l {0}
+        run: |
+          cd misc/one_click_macos
+          . ./create_installer_macos.sh
+      - name: Test installer for MacOS
+        shell: bash -l {0}
+        run: |
+          sudo installer -pkg misc/one_click_macos/dist/alphamap_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: misc/one_click_macos/dist/alphamap_gui_installer_macos.pkg
+          asset_name: alphamap_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 misc/one_click_windows
+          . ./create_installer_windows.sh
+      - name: Test installer for Windows
+        shell: bash -l {0}
+        run: |
+          cd misc/one_click_windows/dist/
+          echo "TODO, this test seems to freeze the runner..."
+          # ./alphamap_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: misc/one_click_windows/dist/alphamap_installer_windows.exe
+          asset_name: alphamap_installer_windows.exe
+          asset_content_type: application/octet-stream

README.md

@@ -37,14 +37,19 @@ The GUI of AlphaMap is a completely stand-alone tool that requires no knowledge
 
 AlphaMap can be installed in an existing Python 3.8 environment with a single `bash` command. *This `bash` command can also be run directly from within a Jupyter notebook by prepending it with a `!`*.
 
+```bash
+pip install alphamap[stable]
+```
+The [stable] tag ensures you get the latest stable release with fixed dependencies. However, it can be omitted if you prefer more flexible dependency versions:
+
 ```bash
 pip install alphamap
 ```
 
 When a new version of AlphaMap becomes available, the old version can easily be upgraded by running e.g. the command again with an additional `--upgrade` flag:
 
 ```bash
-pip install alphamap --upgrade
+pip install --upgrade alphamap[stable] 
 ```
 
 NOTE: When installing with `pip`, UniProt information is not included. Upon first usage of a specific Organism, its information will be automatically downloaded from UniProt.
@@ -71,11 +76,13 @@ For any Python package, it is highly recommended to use a [conda virtual environ
 ```bash
 conda create -n alphamap python=3.8 -y
 conda activate alphamap
-pip install -e .
+pip install -e ".[stable]"
 ```
 
 * By using the editable flag `-e`, all modifications to the AlphaMap [source code folder](alphamap) are directly reflected when running AlphaMap. Note that the AlphaMap folder cannot be moved and/or renamed if an editable version is installed.
 
+* The [stable] tag ensures you get the latest stable release with fixed dependencies. However, it can be omitted if you prefer more flexible dependency versions.
+
 * When using Jupyter notebooks and multiple conda environments direcly from the terminal, it is recommended to `conda install nb_conda_kernels` in the conda base environment. Hereafter, running a `jupyter notebook` from the conda base environment should have a `python [conda env: alphamap]` kernel available, in addition to all other conda kernels in which the command `conda install ipykernel` was run.
 
 

alphamap/__init__.py

@@ -1 +1 @@
-__version__ = "0.1.10"
+__version__ = "0.1.11"