Merge pull request #436 from Dana-Farber-AIOS/dev-mamba

Converting to mamba

.github/workflows/tests-linux.yml

@@ -34,34 +34,35 @@ jobs:
         sudo apt-get update
         sudo apt-get install openslide-tools
         sudo apt-get install pandoc
-    - name: Setup Miniconda
-      uses: conda-incubator/setup-miniconda@v2
+    - name: Setup Micromamba
+      uses: mamba-org/setup-micromamba@v1
       with:
-        auto-activate-base: false
-        activate-environment: pathml
+        micromamba-version: '1.5.6-0'
+        environment-name: pathml
         environment-file: requirements/environment_test.yml
-        # mamba-version: "*"
-        miniforge-version: latest
-        use-mamba: true
-        channels: conda-forge
-        python-version: ${{ matrix.python-version }}
+        init-shell: >-
+          bash
+        create-args: >-
+          python=${{ matrix.python-version }}
     - name: Debugging
       run: |
         echo "Printing the environment.yml file..."
         cat requirements/environment_test.yml
-        echo "Checking the status of mamba..."
-        mamba --version
+        echo "Checking the status of micro mamba..."
+        micromamba config
         echo "Checking the available disk space..."
         df -h
         
-    - name: Install dependencies with mamba
-      shell: bash -l {0}
-      run: mamba env update --file requirements/environment_test.yml --name pathml
-    - name: Conda info
+    # - name: Install dependencies with micromamba
+    #   shell: bash -l {0}
+    #   run: micromamba env update --file requirements/environment_test.yml --name pathml
+
+    - name: Micromamba info
       shell: bash -l {0}
       run: |
-        conda info
-        conda list
+        micromamba info
+        micromamba config
+        micromamba list
     
     - name: Set default Temurin JDK 17
       run: |

.github/workflows/tests-macos.yml

@@ -17,33 +17,34 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-latest]
-        python-version: ["3.8"]
+        python-version: ["3.8", "3.9", "3.10"]
 
     steps:
       - uses: actions/checkout@v2
 
       - name: Install openslide
         shell: bash -l {0}
         run: brew install openslide
+
 
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Setup Micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          auto-update-conda: true
-          miniforge-version: latest
-          use-mamba: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: pathml
+          micromamba-version: '1.5.6-0'
+          environment-name: pathml
           environment-file: requirements/environment_mac.yml
-          channels: conda-forge
+          init-shell: >-
+            bash
+          create-args: >-
+            python=${{ matrix.python-version }}
 
-      - name: Conda info
-        shell: bash -l {0}
-        run: conda info
 
-      - name: Conda Version
+      - name: Micromamba info
         shell: bash -l {0}
-        run: conda --version
+        run: |
+          micromamba info
+          micromamba config
+          micromamba list
 
       - name: Set default Temurin JDK 17
         run: |

.github/workflows/tests-windows.yml

@@ -40,21 +40,18 @@ jobs:
         run: echo "JDK_HOME=${JAVA_HOME}" >> $GITHUB_ENV
         shell: bash
 
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+
+      - name: Setup Micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          auto-activate-base: false
-          activate-environment: pathml
+          micromamba-version: '1.5.6-0'
+          environment-name: pathml
           environment-file: environment.yml
-          # environment-file: '.github/ci-environments/env-py39.yml'
-          # environment-file: .github/ci-environments/env-py${{ matrix.python-version == '3.10' && '310' || matrix.python-version == '3.9' && '39' || '38' }}.yml
-          mamba-version: "*"
-          python-version: ${{ matrix.python-version }}
-
-      # - name: Install JavaBridge and other dependencies
-      #   shell: bash -l {0}
-      #   run: |
-      #     pip install python-javabridge
+          init-shell: >-
+            bash
+          create-args: >-
+            python=${{ matrix.python-version }}
+
 
       - name: Run Python script to find JVM path
         shell: bash -l {0}
@@ -91,11 +88,12 @@ jobs:
         env:
           OPENSLIDE_PATH: ${{ env.OPENSLIDE_PATH }}
 
-      - name: Conda info
+      - name: Mamba info
         shell: bash -l {0}
         run: |
-          conda info
-          conda list
+          micromamba info
+          micromamba config
+          micromamba list
 
       - name: Install PathML
         shell: bash -l {0}      

README.md

@@ -56,13 +56,25 @@ View the official [PathML Documentation on readthedocs](https://pathml.readthedo
 
 ## 1.1 Prerequisites
 
-We recommend using [Conda](https://conda.io/projects/conda/en/latest/user-guide/getting-started.html#) for managing your environments. 
+We recommend using [Micromamba](https://mamba.readthedocs.io/en/latest/index.html) for managing your environments. We provide instructions on how to install PathML via Micromamba below. In addition, we also provide instructions on how to install via [Miniconda](https://docs.conda.io/en/latest/miniconda.html) should you have a license. 
 
-#### Installing Conda
+#### Installation 
 
-If you don't have Conda installed, you can download Miniconda [here](https://docs.conda.io/en/latest/miniconda.html).
+If you don't have Miniconda installed, you can download Miniconda [here](https://docs.conda.io/en/latest/miniconda.html).
 
-#### Updating Conda and Using libmamba (Optional)
+
+#### Upating Micromamba
+
+Make sure you have the recent version of Micromamba by using the following command:
+```
+micromamba update 
+```
+
+####  Updating Conda and Using libmamba (Optional)
+
+**If you are using Micromamba, you can skip to the next [section](#Platform-Specific-External-Dependencies).** 
+
+ We recommend that Anaconda/Microconda users complete the following steps to update your Conda version and use `libmamba` to resolve dependency conflicts. 
 
 Recent versions of Conda have integrated `libmamba`, a faster dependency solver. To benefit from this improvement, first ensure your Conda is updated:
 
@@ -80,7 +92,7 @@ conda config --set solver libmamba
 
 #### Platform-Specific External Dependencies
 
-For installation methods [1)](#2.1-Install-with-pip-(Recommended-for-Users)) and [2)](#2.2-Install-from-Source-(Recommended-for-Developers)), you will need to install the following platform-specific packages. 
+For installation methods [1)](#2.1-Install-with-Micromamba-and-pip-(Recommended-for-Users)) and [2)](#2.2-Install-from-Source-(Recommended-for-Developers)), you will need to install the following platform-specific packages. 
 
 * Linux: Install external dependencies with [Apt](https://ubuntu.com/server/docs/package-management):
 ````
@@ -108,7 +120,20 @@ For Windows users, an alternative to using `vcpkg` is to download and use pre-bu
 
 ## 1.2 PathML Installation Methods
 
-### 1.2.1 Install with pip (Recommended for Users)
+### 1.2.1 Install with Micromamba and pip (Recommended for Users)
+
+#### Create and Activate Micromamba Environment and install openjdk
+````
+micromamba create -n pathml  'openjdk<=18.0' -c conda-forge python=3.9
+micromamba activate pathml
+````
+
+#### Install `PathML` from PyPI
+````
+pip install pathml
+````
+
+### 1.2.2 Install with Anaconda and pip 
 
 #### Create and Activate Conda Environment
 ````
@@ -125,7 +150,7 @@ conda install -c conda-forge 'openjdk<=18.0'
 pip install pathml
 ````
 
-### 1.2.2 Install from Source (Recommended for Developers)
+### 1.2.3 Install from Source (Recommended for Developers)
 
 #### Clone repository
 ````
@@ -155,7 +180,7 @@ conda activate pathml
 pip install -e .
 ````
 
-### 1.2.3 Use Docker Container
+### 1.2.4 Use Docker Container
 
 First, download or build the PathML Docker container:
 
@@ -192,7 +217,7 @@ Note that these instructions assume that there are no other processes using port
 Please refer to the `Docker run` [documentation](https://docs.docker.com/engine/reference/run/) for further instructions
 on accessing the container, e.g. for mounting volumes to access files on a local machine from within the container.
 
-### 1.2.4 Use Google Colab
+### 1.2.5 Use Google Colab
 
 To get PathML running in a Colab environment:
 

requirements/environment_mac.yml

@@ -8,6 +8,7 @@ dependencies:
     - python<=3.10
     - pip==23.3.2
     - numpy==1.23.5
+    - python-javabridge==4.0.3
     - scipy<=1.11.4
     - scikit-image<=0.22.0
     - matplotlib<=3.8.2
@@ -20,9 +21,11 @@ dependencies:
     - coverage==7.3.4
     - networkx<=3.2.1
     - pip:
+        # - setuptools==58.2.0
+        # - numpy==1.23.5
         - torch==1.13.1
         - python-bioformats==4.0.7
-        - python-javabridge==4.0.3
+        # - python-javabridge==4.0.3
         - protobuf==3.20.3
         - onnx==1.15.0
         - onnxruntime==1.16.3