From 079a240924f07e2b894f822d6315d47ccb34833e Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 08:38:44 -0700
Subject: [PATCH 01/30] first attempt at adding micromamba to windows

---
 .github/workflows/tests-windows.yml | 23 ++++++++++-------------
 1 file changed, 10 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/tests-windows.yml b/.github/workflows/tests-windows.yml
index a53631b3..09214265 100644
--- a/.github/workflows/tests-windows.yml
+++ b/.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}

From b92b153b4a3c515f40070893ac35e87d5807e98b Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 08:56:52 -0700
Subject: [PATCH 02/30] replace conda info step with mamba info

---
 .github/workflows/tests-windows.yml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/tests-windows.yml b/.github/workflows/tests-windows.yml
index 09214265..f85dca42 100644
--- a/.github/workflows/tests-windows.yml
+++ b/.github/workflows/tests-windows.yml
@@ -51,7 +51,7 @@ jobs:
             bash
           create-args: >-
             python=${{ matrix.python-version }}
-            
+
 
       - name: Run Python script to find JVM path
         shell: bash -l {0}
@@ -88,11 +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}      

From e3645194d92ab6eff894f1fb64cc7533f4bfff13 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 10:09:20 -0700
Subject: [PATCH 03/30] testing changed linux file

---
 .github/workflows/tests-linux.yml | 29 +++++++++++++++--------------
 1 file changed, 15 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/tests-linux.yml b/.github/workflows/tests-linux.yml
index 3b60d160..34f9aa61 100644
--- a/.github/workflows/tests-linux.yml
+++ b/.github/workflows/tests-linux.yml
@@ -34,17 +34,16 @@ 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
-        environment-file: requirements/environment_test.yml
-        # mamba-version: "*"
-        miniforge-version: latest
-        use-mamba: true
-        channels: conda-forge
-        python-version: ${{ matrix.python-version }}
+        micromamba-version: '1.5.6-0'
+        environment-name: pathml
+        environment-file: environment.yml
+        init-shell: >-
+          bash
+        create-args: >-
+          python=${{ matrix.python-version }}
     - name: Debugging
       run: |
         echo "Printing the environment.yml file..."
@@ -56,12 +55,14 @@ jobs:
         
     - name: Install dependencies with mamba
       shell: bash -l {0}
-      run: mamba env update --file requirements/environment_test.yml --name pathml
-    - name: Conda info
+      run: micromamba env update --file requirements/environment_test.yml --name pathml
+    
+    - name: Mamba info
       shell: bash -l {0}
       run: |
-        conda info
-        conda list
+        micromamba info
+        micromamba config
+        micromamba list
     
     - name: Set default Temurin JDK 17
       run: |

From de956c7b64f0011d633ce46808be0e9ef3a29439 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 10:27:48 -0700
Subject: [PATCH 04/30] fixing mamba command for linux file

---
 .github/workflows/tests-linux.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/tests-linux.yml b/.github/workflows/tests-linux.yml
index 34f9aa61..777f7013 100644
--- a/.github/workflows/tests-linux.yml
+++ b/.github/workflows/tests-linux.yml
@@ -48,16 +48,16 @@ jobs:
       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
+    - name: Install dependencies with micromamba
       shell: bash -l {0}
       run: micromamba env update --file requirements/environment_test.yml --name pathml
     
-    - name: Mamba info
+    - name: Micromamba info
       shell: bash -l {0}
       run: |
         micromamba info

From cc5af8835076cc42bd5a39511acd8e00cfaf1a27 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 10:38:52 -0700
Subject: [PATCH 05/30] getting rid of redundant job in linux file

---
 .github/workflows/tests-linux.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/tests-linux.yml b/.github/workflows/tests-linux.yml
index 777f7013..1d862fd6 100644
--- a/.github/workflows/tests-linux.yml
+++ b/.github/workflows/tests-linux.yml
@@ -53,9 +53,9 @@ jobs:
         echo "Checking the available disk space..."
         df -h
         
-    - name: Install dependencies with micromamba
-      shell: bash -l {0}
-      run: micromamba env update --file requirements/environment_test.yml --name pathml
+    # - 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}

From 040e1b59f80a8c14efedd6fc055a38aa3ccad01c Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 11:03:07 -0700
Subject: [PATCH 06/30] changing reference envi file linux

---
 .github/workflows/tests-linux.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests-linux.yml b/.github/workflows/tests-linux.yml
index 1d862fd6..77750fcc 100644
--- a/.github/workflows/tests-linux.yml
+++ b/.github/workflows/tests-linux.yml
@@ -39,7 +39,7 @@ jobs:
       with:
         micromamba-version: '1.5.6-0'
         environment-name: pathml
-        environment-file: environment.yml
+        environment-file: requirements/environment_test.yml
         init-shell: >-
           bash
         create-args: >-

From e0d33c632d919576c7f2e39053279605473ae13a Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 11:29:23 -0700
Subject: [PATCH 07/30] first changes to mac test file

---
 .github/workflows/tests-macos.yml | 31 +++++++++++++++++--------------
 1 file changed, 17 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index e3283443..a33a1631 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -4,9 +4,13 @@ on:
   workflow_dispatch:
   pull_request:
     branches:
+      - dev 
+      - master
       - dev_graph
   push:
     branches:
+      - dev 
+      - master 
       - dev_graph
 
 jobs:
@@ -26,24 +30,23 @@ jobs:
         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
+      - name: Micromamba info
         shell: bash -l {0}
-        run: conda info
-
-      - name: Conda Version
-        shell: bash -l {0}
-        run: conda --version
+        run: |
+          micromamba info
+          micromamba config
+          micromamba list
 
       - name: Set default Temurin JDK 17
         run: |

From 74b6f28e3c49cb99a7ffc96277eec8c5320866c3 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 11:41:08 -0700
Subject: [PATCH 08/30] adjusting environment file for mac

---
 requirements/environment_mac.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/environment_mac.yml b/requirements/environment_mac.yml
index ce968ed9..ac7d709a 100644
--- a/requirements/environment_mac.yml
+++ b/requirements/environment_mac.yml
@@ -19,10 +19,10 @@ dependencies:
     - pre-commit<=3.6.0
     - coverage==7.3.4
     - networkx<=3.2.1
+    - python-javabridge==4.0.3
     - pip:
         - torch==1.13.1
         - python-bioformats==4.0.7
-        - python-javabridge==4.0.3
         - protobuf==3.20.3
         - onnx==1.15.0
         - onnxruntime==1.16.3

From aa196f0cf59c8c95914d8d6f5f28026d8b04545f Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 12:01:28 -0700
Subject: [PATCH 09/30] trying java fix

---
 .github/workflows/tests-macos.yml | 16 ++++++++++++++++
 requirements/environment_mac.yml  |  2 +-
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index a33a1631..0371c64e 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -29,6 +29,22 @@ jobs:
       - name: Install openslide
         shell: bash -l {0}
         run: brew install openslide
+
+      - name: Set up JDK 17
+        uses: actions/setup-java@v2
+        with:
+          java-version: '17'
+          distribution: 'temurin'
+
+      - name: Print JAVA_HOME and PATH
+        run: |
+          echo "JAVA_HOME: $env:JAVA_HOME"
+          echo "PATH: $env:PATH"
+        shell: pwsh
+
+      - name: Set JDK_HOME environment variable
+        run: echo "JDK_HOME=${JAVA_HOME}" >> $GITHUB_ENV
+        shell: bash
       
       - name: Setup Micromamba
         uses: mamba-org/setup-micromamba@v1
diff --git a/requirements/environment_mac.yml b/requirements/environment_mac.yml
index ac7d709a..ce968ed9 100644
--- a/requirements/environment_mac.yml
+++ b/requirements/environment_mac.yml
@@ -19,10 +19,10 @@ dependencies:
     - pre-commit<=3.6.0
     - coverage==7.3.4
     - networkx<=3.2.1
-    - python-javabridge==4.0.3
     - pip:
         - torch==1.13.1
         - python-bioformats==4.0.7
+        - python-javabridge==4.0.3
         - protobuf==3.20.3
         - onnx==1.15.0
         - onnxruntime==1.16.3

From 330f7443fea7562f3ff43a33183c00471adcae11 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 12:32:47 -0700
Subject: [PATCH 10/30] trying pep517 to load python javabridge

---
 .github/workflows/tests-macos.yml | 4 ++++
 requirements/environment_mac.yml  | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index 0371c64e..cab790ed 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -57,6 +57,10 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
 
+      - name: Install python-javabridge
+        shell: bash -l {0}
+        run: pip install --use-pep517 python-javabridge==4.0.3
+
       - name: Micromamba info
         shell: bash -l {0}
         run: |
diff --git a/requirements/environment_mac.yml b/requirements/environment_mac.yml
index ce968ed9..8685a874 100644
--- a/requirements/environment_mac.yml
+++ b/requirements/environment_mac.yml
@@ -22,7 +22,7 @@ dependencies:
     - pip:
         - 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

From b298226008e800fea6ffbd9a03a1d33d8523730b Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 12:40:37 -0700
Subject: [PATCH 11/30] adjusting setuptools depen

---
 .github/workflows/tests-macos.yml | 6 +++---
 requirements/environment_mac.yml  | 3 ++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index cab790ed..73a52575 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -57,9 +57,9 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
 
-      - name: Install python-javabridge
-        shell: bash -l {0}
-        run: pip install --use-pep517 python-javabridge==4.0.3
+      # - name: Install python-javabridge
+      #   shell: bash -l {0}
+      #   run: pip install --use-pep517 python-javabridge==4.0.3
 
       - name: Micromamba info
         shell: bash -l {0}
diff --git a/requirements/environment_mac.yml b/requirements/environment_mac.yml
index 8685a874..ebf44eb1 100644
--- a/requirements/environment_mac.yml
+++ b/requirements/environment_mac.yml
@@ -20,9 +20,10 @@ dependencies:
     - coverage==7.3.4
     - networkx<=3.2.1
     - pip:
+        - setuptools==58.2.0
         - 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

From e37e868c1737cc8d4801bd8bbdcfcec9b809a09f Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 12:58:27 -0700
Subject: [PATCH 12/30] installing bioformats and javabridge sep

---
 .github/workflows/tests-macos.yml | 10 +++++++---
 requirements/environment_mac.yml  |  6 +++---
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index 73a52575..5f5c3090 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -57,9 +57,13 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
 
-      # - name: Install python-javabridge
-      #   shell: bash -l {0}
-      #   run: pip install --use-pep517 python-javabridge==4.0.3
+      - name: Install python-javabridge
+        shell: bash -l {0}
+        run: pip install --use-pep517 python-javabridge==4.0.3
+
+      - name: Install python-bioformats
+        shell: bash -l {0}
+        run: pip install python-bioformats==4.0.7
 
       - name: Micromamba info
         shell: bash -l {0}
diff --git a/requirements/environment_mac.yml b/requirements/environment_mac.yml
index ebf44eb1..6b0f0a7a 100644
--- a/requirements/environment_mac.yml
+++ b/requirements/environment_mac.yml
@@ -20,10 +20,10 @@ dependencies:
     - coverage==7.3.4
     - networkx<=3.2.1
     - pip:
-        - setuptools==58.2.0
+        # - setuptools==58.2.0
         - torch==1.13.1
-        - python-bioformats==4.0.7
-        - python-javabridge==4.0.3
+        # - python-bioformats==4.0.7
+        # - python-javabridge==4.0.3
         - protobuf==3.20.3
         - onnx==1.15.0
         - onnxruntime==1.16.3

From 401a28487ccc9cf4c62f347d82c76c167b7c228f Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 13:08:27 -0700
Subject: [PATCH 13/30] trying new way to install javabridge

---
 .github/workflows/tests-macos.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index 5f5c3090..c249da62 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -59,7 +59,8 @@ jobs:
 
       - name: Install python-javabridge
         shell: bash -l {0}
-        run: pip install --use-pep517 python-javabridge==4.0.3
+        # run: pip install --use-pep517 python-javabridge==4.0.3
+        run: pip install python-javabridge==4.0.3
 
       - name: Install python-bioformats
         shell: bash -l {0}

From 76d780fba00908bdfaa469e4c8157e7f493c55a6 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 13:14:01 -0700
Subject: [PATCH 14/30] trying adding numpy to pep517 statement

---
 .github/workflows/tests-macos.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index c249da62..9ff2d694 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -59,8 +59,8 @@ jobs:
 
       - name: Install python-javabridge
         shell: bash -l {0}
-        # run: pip install --use-pep517 python-javabridge==4.0.3
-        run: pip install python-javabridge==4.0.3
+        run: pip install --use-pep517 numpy==1.23.5 python-javabridge==4.0.3
+        # run: pip install python-javabridge==4.0.3
 
       - name: Install python-bioformats
         shell: bash -l {0}

From ba805b32013330a478e61a448aa00ed2f24e4779 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 13:19:52 -0700
Subject: [PATCH 15/30] taking out initial java jobs

---
 .github/workflows/tests-macos.yml | 19 ++-----------------
 1 file changed, 2 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index 9ff2d694..ea550250 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -30,21 +30,6 @@ jobs:
         shell: bash -l {0}
         run: brew install openslide
 
-      - name: Set up JDK 17
-        uses: actions/setup-java@v2
-        with:
-          java-version: '17'
-          distribution: 'temurin'
-
-      - name: Print JAVA_HOME and PATH
-        run: |
-          echo "JAVA_HOME: $env:JAVA_HOME"
-          echo "PATH: $env:PATH"
-        shell: pwsh
-
-      - name: Set JDK_HOME environment variable
-        run: echo "JDK_HOME=${JAVA_HOME}" >> $GITHUB_ENV
-        shell: bash
       
       - name: Setup Micromamba
         uses: mamba-org/setup-micromamba@v1
@@ -59,8 +44,8 @@ jobs:
 
       - name: Install python-javabridge
         shell: bash -l {0}
-        run: pip install --use-pep517 numpy==1.23.5 python-javabridge==4.0.3
-        # run: pip install python-javabridge==4.0.3
+        # run: pip install --use-pep517 numpy==1.23.5 python-javabridge==4.0.3
+        run: pip install python-javabridge==4.0.3
 
       - name: Install python-bioformats
         shell: bash -l {0}

From cf00acc4541781ee68513ea318ab327a031ef88a Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 13:28:33 -0700
Subject: [PATCH 16/30] adding 3.9 and .10 to python

---
 .github/workflows/tests-macos.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index ea550250..2d791197 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -21,7 +21,7 @@ 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

From 36208e2db97fe0088432b844bd43f94c8e9efde0 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 13:46:11 -0700
Subject: [PATCH 17/30] trying javabridge instead of python-javabridge

---
 .github/workflows/tests-macos.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index 2d791197..12d875f5 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -45,7 +45,8 @@ jobs:
       - name: Install python-javabridge
         shell: bash -l {0}
         # run: pip install --use-pep517 numpy==1.23.5 python-javabridge==4.0.3
-        run: pip install python-javabridge==4.0.3
+        # run: pip install python-javabridge==4.0.3
+        run: pip install javabridge==1.0.19
 
       - name: Install python-bioformats
         shell: bash -l {0}

From 0c3212c026af5b9eefea16921d0e9f12736c721f Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Thu, 15 Aug 2024 13:58:22 -0700
Subject: [PATCH 18/30] trying download of python-javabridge from git

---
 .github/workflows/tests-macos.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index 12d875f5..3f945134 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -46,7 +46,7 @@ jobs:
         shell: bash -l {0}
         # run: pip install --use-pep517 numpy==1.23.5 python-javabridge==4.0.3
         # run: pip install python-javabridge==4.0.3
-        run: pip install javabridge==1.0.19
+        run: pip install git+https://github.com/LeeKamentsky/python-javabridge
 
       - name: Install python-bioformats
         shell: bash -l {0}

From e41ad3ef924b9df2119148ba1d1271bfccc10ef1 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Fri, 16 Aug 2024 09:17:55 -0700
Subject: [PATCH 19/30] adding javabridge back to main environment file

---
 .github/workflows/tests-macos.yml | 10 ----------
 requirements/environment_mac.yml  |  4 ++--
 2 files changed, 2 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index 3f945134..a7223c23 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -42,16 +42,6 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
 
-      - name: Install python-javabridge
-        shell: bash -l {0}
-        # run: pip install --use-pep517 numpy==1.23.5 python-javabridge==4.0.3
-        # run: pip install python-javabridge==4.0.3
-        run: pip install git+https://github.com/LeeKamentsky/python-javabridge
-
-      - name: Install python-bioformats
-        shell: bash -l {0}
-        run: pip install python-bioformats==4.0.7
-
       - name: Micromamba info
         shell: bash -l {0}
         run: |
diff --git a/requirements/environment_mac.yml b/requirements/environment_mac.yml
index 6b0f0a7a..1006b518 100644
--- a/requirements/environment_mac.yml
+++ b/requirements/environment_mac.yml
@@ -22,8 +22,8 @@ dependencies:
     - pip:
         # - setuptools==58.2.0
         - torch==1.13.1
-        # - python-bioformats==4.0.7
-        # - python-javabridge==4.0.3
+        - python-bioformats==4.0.7
+        - python-javabridge==4.0.3
         - protobuf==3.20.3
         - onnx==1.15.0
         - onnxruntime==1.16.3

From ef32ccec8c6e22ad81a139babea2172b3535c015 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Fri, 16 Aug 2024 09:47:19 -0700
Subject: [PATCH 20/30] adding new readme

---
 README.md | 43 ++++++++++++++++++++++++++++++++++---------
 1 file changed, 34 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index 97fd5a38..ad2086f3 100644
--- a/README.md
+++ b/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)](#1.2.2-Install-with-Anaconda and-pip) and [2)](#1.2.3-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:
 

From f153b4eddc8636196b7f22fec64e02ad384b49af Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Fri, 16 Aug 2024 09:49:14 -0700
Subject: [PATCH 21/30] adjusting sections

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index ad2086f3..f016a178 100644
--- a/README.md
+++ b/README.md
@@ -70,7 +70,7 @@ Make sure you have the recent version of Micromamba by using the following comma
 micromamba update 
 ```
 
-#####  Updating Conda and Using libmamba (Optional)
+####  Updating Conda and Using libmamba (Optional)
 
 **If you are using Micromamba, you can skip to the next [section](#Platform-Specific-External-Dependencies).** 
 

From b6c66cb55ee2e9095d2e98fa2c16b89faae9102f Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Fri, 16 Aug 2024 09:53:44 -0700
Subject: [PATCH 22/30] adjusting links

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index f016a178..01998ad5 100644
--- a/README.md
+++ b/README.md
@@ -92,7 +92,7 @@ conda config --set solver libmamba
 
 #### Platform-Specific External Dependencies
 
-For installation methods [1)](#1.2.2-Install-with-Anaconda and-pip) and [2)](#1.2.3-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):
 ````

From e78468c009dfacb3495f1519383b6738dc49983b Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Fri, 16 Aug 2024 10:31:12 -0700
Subject: [PATCH 23/30] trying to install numpy first

---
 .github/workflows/tests-macos.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index a7223c23..4b2ac07d 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -42,6 +42,14 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
 
+      - name: Install NumPy
+        shell: bash -l {0}      
+        run: pip install numpy==1.23.5
+
+      - name: Install Python-Javabridge
+        shell: bash -l {0}      
+        run: pip install python-javabridge==4.0.3
+
       - name: Micromamba info
         shell: bash -l {0}
         run: |

From 783d780621c60615af4bd4b78e9c61038ad26b21 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Fri, 16 Aug 2024 10:36:05 -0700
Subject: [PATCH 24/30] changing order in the environment file

---
 requirements/environment_mac.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/environment_mac.yml b/requirements/environment_mac.yml
index 1006b518..99f4bbcb 100644
--- a/requirements/environment_mac.yml
+++ b/requirements/environment_mac.yml
@@ -23,7 +23,7 @@ dependencies:
         # - setuptools==58.2.0
         - 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

From 34d87475ffa19ca2871478dd4c6e90a7ef6b32b3 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Fri, 16 Aug 2024 10:43:48 -0700
Subject: [PATCH 25/30] reordering pip statements

---
 .github/workflows/tests-macos.yml | 8 --------
 requirements/environment_mac.yml  | 5 +++--
 2 files changed, 3 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index 4b2ac07d..a7223c23 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -42,14 +42,6 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
 
-      - name: Install NumPy
-        shell: bash -l {0}      
-        run: pip install numpy==1.23.5
-
-      - name: Install Python-Javabridge
-        shell: bash -l {0}      
-        run: pip install python-javabridge==4.0.3
-
       - name: Micromamba info
         shell: bash -l {0}
         run: |
diff --git a/requirements/environment_mac.yml b/requirements/environment_mac.yml
index 99f4bbcb..f715ceb5 100644
--- a/requirements/environment_mac.yml
+++ b/requirements/environment_mac.yml
@@ -7,7 +7,7 @@ channels:
 dependencies:
     - python<=3.10
     - pip==23.3.2
-    - numpy==1.23.5
+    # - numpy==1.23.5
     - scipy<=1.11.4
     - scikit-image<=0.22.0
     - matplotlib<=3.8.2
@@ -21,9 +21,10 @@ dependencies:
     - 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

From fbaf12c2c18f1142d9adae549acb946b232901f0 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Fri, 16 Aug 2024 10:50:45 -0700
Subject: [PATCH 26/30] taking bioformats and javabridge out of main
 environment file mac

---
 .github/workflows/tests-macos.yml | 4 ++++
 requirements/environment_mac.yml  | 4 ++--
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index a7223c23..a37f3d72 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -42,6 +42,10 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
 
+      - name: Install python-javabridge and python-bioformats
+        shell: bash -l {0}      
+        run: pip install python-javabridge==4.0.3 python-bioformats==4.0.7
+
       - name: Micromamba info
         shell: bash -l {0}
         run: |
diff --git a/requirements/environment_mac.yml b/requirements/environment_mac.yml
index f715ceb5..5ddc2aa7 100644
--- a/requirements/environment_mac.yml
+++ b/requirements/environment_mac.yml
@@ -23,8 +23,8 @@ dependencies:
         # - setuptools==58.2.0
         - numpy==1.23.5
         - torch==1.13.1
-        - python-bioformats==4.0.7
-        - python-javabridge==4.0.3
+        # - python-bioformats==4.0.7
+        # - python-javabridge==4.0.3
         - protobuf==3.20.3
         - onnx==1.15.0
         - onnxruntime==1.16.3

From 185909582ed999622ab5bfbe5a9355c69696ff16 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Fri, 16 Aug 2024 10:58:41 -0700
Subject: [PATCH 27/30] trying to install javabridge from github

---
 .github/workflows/tests-macos.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index a37f3d72..f7858b69 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -44,7 +44,7 @@ jobs:
 
       - name: Install python-javabridge and python-bioformats
         shell: bash -l {0}      
-        run: pip install python-javabridge==4.0.3 python-bioformats==4.0.7
+        run: pip install git+https://github.com/LeeKamentsky/python-javabridge.git python-javabridge==4.0.3 python-bioformats==4.0.7
 
       - name: Micromamba info
         shell: bash -l {0}

From 4772b462c606d273917779221a46c36200e71f36 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Fri, 16 Aug 2024 11:43:23 -0700
Subject: [PATCH 28/30] changing channel for javabridge

---
 .github/workflows/tests-macos.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index f7858b69..7c85b3b9 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -44,7 +44,11 @@ jobs:
 
       - name: Install python-javabridge and python-bioformats
         shell: bash -l {0}      
-        run: pip install git+https://github.com/LeeKamentsky/python-javabridge.git python-javabridge==4.0.3 python-bioformats==4.0.7
+        run: micromamba install python-javabridge==4.0.3 -c conda-forge/osx-64/
+
+      - name: Install python-bioformats
+        shell: bash -l {0}      
+        run: pip install python-bioformats==4.0.7
 
       - name: Micromamba info
         shell: bash -l {0}

From dc0847cea5d283e6254822aa917d961ddc17fc83 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Fri, 16 Aug 2024 11:55:27 -0700
Subject: [PATCH 29/30] changing which packages are pulled from pip

---
 .github/workflows/tests-macos.yml | 7 -------
 requirements/environment_mac.yml  | 7 ++++---
 2 files changed, 4 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index 7c85b3b9..11425207 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -42,13 +42,6 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
 
-      - name: Install python-javabridge and python-bioformats
-        shell: bash -l {0}      
-        run: micromamba install python-javabridge==4.0.3 -c conda-forge/osx-64/
-
-      - name: Install python-bioformats
-        shell: bash -l {0}      
-        run: pip install python-bioformats==4.0.7
 
       - name: Micromamba info
         shell: bash -l {0}
diff --git a/requirements/environment_mac.yml b/requirements/environment_mac.yml
index 5ddc2aa7..851adc99 100644
--- a/requirements/environment_mac.yml
+++ b/requirements/environment_mac.yml
@@ -7,7 +7,8 @@ channels:
 dependencies:
     - python<=3.10
     - pip==23.3.2
-    # - numpy==1.23.5
+    - numpy==1.23.5
+    - python-javabridge==4.0.3
     - scipy<=1.11.4
     - scikit-image<=0.22.0
     - matplotlib<=3.8.2
@@ -21,9 +22,9 @@ dependencies:
     - networkx<=3.2.1
     - pip:
         # - setuptools==58.2.0
-        - numpy==1.23.5
+        # - numpy==1.23.5
         - torch==1.13.1
-        # - python-bioformats==4.0.7
+        - python-bioformats==4.0.7
         # - python-javabridge==4.0.3
         - protobuf==3.20.3
         - onnx==1.15.0

From 42cba7da3fc5641a248fc69e368aef9783e7b970 Mon Sep 17 00:00:00 2001
From: jamesgwen <jgw787@gmail.com>
Date: Mon, 19 Aug 2024 10:14:14 -0700
Subject: [PATCH 30/30] adjusting test file macos

---
 .github/workflows/tests-macos.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
index 11425207..348a044c 100644
--- a/.github/workflows/tests-macos.yml
+++ b/.github/workflows/tests-macos.yml
@@ -4,13 +4,9 @@ on:
   workflow_dispatch:
   pull_request:
     branches:
-      - dev 
-      - master
       - dev_graph
   push:
     branches:
-      - dev 
-      - master 
       - dev_graph
 
 jobs: