From f30d9fcae245bab3772c7ea9ff4d3622f4c3ee39 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+behxyz@users.noreply.github.com>
Date: Mon, 3 May 2021 12:25:02 -0400
Subject: [PATCH 01/14] Add CuPy dependency

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>
---
 requirements-dev.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements-dev.txt b/requirements-dev.txt
index 268dfb87d7..9e03935242 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -32,3 +32,4 @@ sphinx-autodoc-typehints==1.11.1
 sphinx-rtd-theme==0.5.2
 cucim~=0.19.0; platform_system == "Linux"
 openslide-python==1.1.2
+cupy==8.6.0

From be0d7a536fae366cf3791ffc7a16ceb74f75e650 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+behxyz@users.noreply.github.com>
Date: Mon, 3 May 2021 12:25:04 -0400
Subject: [PATCH 02/14] Remove CUDA-based dependencies (only cupy for now)

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>
---
 .github/workflows/pythonapp.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index 8f7d9c72c2..6f279cd278 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -77,6 +77,9 @@ jobs:
       with:
         path: ${{ steps.pip-cache.outputs.dir }}
         key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
+    - name: Remove CUDA-required dependencies
+      run: |
+        python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines([t for t in txt if not t.startswith('cupy')]); f.close()"
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |

From 6c1feb40d05600e7ffb4ec8f14142b5fd481cb72 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+behxyz@users.noreply.github.com>
Date: Mon, 3 May 2021 12:36:08 -0400
Subject: [PATCH 03/14] Exclude CUDA-based dependecies from flake8-py3

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>
---
 .github/workflows/pythonapp.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index 6f279cd278..62b4fafc01 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -30,6 +30,9 @@ jobs:
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
+    - name: Remove CUDA-required dependencies
+      run: |
+        python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines([t for t in txt if not t.startswith('cupy')]); f.close()"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip wheel

From e8dd7e93dc2fae6cab398aca27df746a158ea9fa Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+behxyz@users.noreply.github.com>
Date: Mon, 3 May 2021 13:47:04 -0400
Subject: [PATCH 04/14] Install CuPy binary specific to each CUDA version

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>
---
 .github/workflows/pythonapp.yml | 5 +++--
 requirements-dev.txt            | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index 62b4fafc01..f8eaf5e669 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -32,7 +32,7 @@ jobs:
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Remove CUDA-required dependencies
       run: |
-        python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines([t for t in txt if not t.startswith('cupy')]); f.close()"
+        sed -i '/^cupy/d' requirements-dev.txt
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip wheel
@@ -82,7 +82,7 @@ jobs:
         key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Remove CUDA-required dependencies
       run: |
-        python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines([t for t in txt if not t.startswith('cupy')]); f.close()"
+        sed -i '/^cupy/d' requirements-dev.txt
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
@@ -286,6 +286,7 @@ jobs:
         which python
         python -m pip install --upgrade pip wheel
         python -m pip install ${{ matrix.pytorch }}
+        sed -i 's/cupy=/cupy-${{ matrix.environment }:-7}=/g' requirements-dev.txt
         python -m pip install -r requirements-dev.txt
         python -m pip list
     - name: Run quick tests (GPU)
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 9e03935242..e07f39d982 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -32,4 +32,4 @@ sphinx-autodoc-typehints==1.11.1
 sphinx-rtd-theme==0.5.2
 cucim~=0.19.0; platform_system == "Linux"
 openslide-python==1.1.2
-cupy==8.6.0
+cupy==9.0.0

From f988530cdbb972bcff2a168e3c7069f14ce8c99a Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+behxyz@users.noreply.github.com>
Date: Mon, 3 May 2021 14:59:42 -0400
Subject: [PATCH 05/14] Make cupy package name lowercase

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>
---
 .github/workflows/pythonapp.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index f8eaf5e669..5aef3f1d8d 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -286,7 +286,7 @@ jobs:
         which python
         python -m pip install --upgrade pip wheel
         python -m pip install ${{ matrix.pytorch }}
-        sed -i 's/cupy=/cupy-${{ matrix.environment }:-7}=/g' requirements-dev.txt
+        sed -i 's/cupy=/cupy-cuda${{ matrix.environment }: -3}=/g' requirements-dev.txt
         python -m pip install -r requirements-dev.txt
         python -m pip list
     - name: Run quick tests (GPU)

From f50778346a014de25a46c131cb13f6ed5c027a7e Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+behxyz@users.noreply.github.com>
Date: Mon, 3 May 2021 19:45:05 -0400
Subject: [PATCH 06/14] Correct matrix environment substring extraction

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>
---
 .github/workflows/pythonapp.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index 5aef3f1d8d..e28a0929ed 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -286,7 +286,8 @@ jobs:
         which python
         python -m pip install --upgrade pip wheel
         python -m pip install ${{ matrix.pytorch }}
-        sed -i 's/cupy=/cupy-cuda${{ matrix.environment }: -3}=/g' requirements-dev.txt
+        matenv=${{ matrix.environment }}
+        sed -i 's/cupy=/cupy-cuda${matenv: -3}=/g' requirements-dev.txt
         python -m pip install -r requirements-dev.txt
         python -m pip list
     - name: Run quick tests (GPU)

From 8fb305bfed7d564a2e3e5b80849370ffa8771bce Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+behxyz@users.noreply.github.com>
Date: Mon, 3 May 2021 20:51:39 -0400
Subject: [PATCH 07/14] Make sed work on Mac too

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>
---
 .github/workflows/pythonapp.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index e28a0929ed..8232145e74 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -32,7 +32,7 @@ jobs:
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Remove CUDA-required dependencies
       run: |
-        sed -i '/^cupy/d' requirements-dev.txt
+        sed -i.bak -e "/^cupy/d" requirements-dev.txt
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip wheel
@@ -82,7 +82,7 @@ jobs:
         key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Remove CUDA-required dependencies
       run: |
-        sed -i '/^cupy/d' requirements-dev.txt
+        sed -i.bak -e "/^cupy/d" requirements-dev.txt
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
@@ -287,7 +287,7 @@ jobs:
         python -m pip install --upgrade pip wheel
         python -m pip install ${{ matrix.pytorch }}
         matenv=${{ matrix.environment }}
-        sed -i 's/cupy=/cupy-cuda${matenv: -3}=/g' requirements-dev.txt
+        sed -i.bak -e "s/cupy=/cupy-cuda${matenv: -3}=/g" requirements-dev.txt
         python -m pip install -r requirements-dev.txt
         python -m pip list
     - name: Run quick tests (GPU)

From 1d81bcbb1b1791bf00fd5b9f4114cb9dc48b9fff Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+behxyz@users.noreply.github.com>
Date: Mon, 3 May 2021 21:24:11 -0400
Subject: [PATCH 08/14] Exclude windows from cupy logic

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>
---
 .github/workflows/pythonapp.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index 8232145e74..fa1824a252 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -80,7 +80,8 @@ jobs:
       with:
         path: ${{ steps.pip-cache.outputs.dir }}
         key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
-    - name: Remove CUDA-required dependencies
+    - if: runner.os != 'windows'
+      name: Remove CUDA-required dependencies (Mac and Linux)
       run: |
         sed -i.bak -e "/^cupy/d" requirements-dev.txt
     - if: runner.os == 'windows'

From 89446c4670b5790ec3c56dabc1a289a1ae22575d Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+behxyz@users.noreply.github.com>
Date: Mon, 3 May 2021 21:25:27 -0400
Subject: [PATCH 09/14] Revert to CuPy 8.6.0 due to availability on PyPI

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>
---
 requirements-dev.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements-dev.txt b/requirements-dev.txt
index e07f39d982..9e03935242 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -32,4 +32,4 @@ sphinx-autodoc-typehints==1.11.1
 sphinx-rtd-theme==0.5.2
 cucim~=0.19.0; platform_system == "Linux"
 openslide-python==1.1.2
-cupy==9.0.0
+cupy==8.6.0

From 8c0bc6de426cdb793d89d3e23fdc9243431080ca Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+behxyz@users.noreply.github.com>
Date: Mon, 3 May 2021 23:36:28 -0400
Subject: [PATCH 10/14] Separate creating CuPy binary dependency from installng
 dependencies

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>
---
 .github/workflows/pythonapp.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index fa1824a252..3cdd20fc1d 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -282,13 +282,16 @@ jobs:
         python get-pip.py && \
         rm get-pip.py;
         fi
+    - name: Create the CUDA-dependent binary requirements for the environment
+      run: |
+        matenv=${{ matrix.environment }}
+        sed -i.bak -e "s/cupy=/cupy-cuda${matenv: -3}=/g" requirements-dev.txt
+        cat "requirements-dev.txt"
     - name: Install dependencies
       run: |
         which python
         python -m pip install --upgrade pip wheel
         python -m pip install ${{ matrix.pytorch }}
-        matenv=${{ matrix.environment }}
-        sed -i.bak -e "s/cupy=/cupy-cuda${matenv: -3}=/g" requirements-dev.txt
         python -m pip install -r requirements-dev.txt
         python -m pip list
     - name: Run quick tests (GPU)

From f1856f0f05a55e28558e6e2b79112f43e92ebc12 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+behxyz@users.noreply.github.com>
Date: Tue, 4 May 2021 00:09:10 -0400
Subject: [PATCH 11/14] Use sed to extract CUDA version

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>
---
 .github/workflows/pythonapp.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index 3cdd20fc1d..adb833ae67 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -284,8 +284,7 @@ jobs:
         fi
     - name: Create the CUDA-dependent binary requirements for the environment
       run: |
-        matenv=${{ matrix.environment }}
-        sed -i.bak -e "s/cupy=/cupy-cuda${matenv: -3}=/g" requirements-dev.txt
+        sed -i.bak -e "s/cupy=/cupy-cuda$(echo ${{ matrix.pytorch }} | sed 's/^.*CUDA//')=/g" requirements-dev.txt
         cat "requirements-dev.txt"
     - name: Install dependencies
       run: |

From a8413bf69beb8ed91bdcbebc078635faaa4c5b56 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+behxyz@users.noreply.github.com>
Date: Tue, 4 May 2021 00:11:28 -0400
Subject: [PATCH 12/14] Fix a typo

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>
---
 .github/workflows/pythonapp.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index adb833ae67..f12e71273c 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -284,7 +284,7 @@ jobs:
         fi
     - name: Create the CUDA-dependent binary requirements for the environment
       run: |
-        sed -i.bak -e "s/cupy=/cupy-cuda$(echo ${{ matrix.pytorch }} | sed 's/^.*CUDA//')=/g" requirements-dev.txt
+        sed -i.bak -e "s/cupy=/cupy-cuda$(echo ${{ matrix.environment }} | sed 's/^.*CUDA//')=/g" requirements-dev.txt
         cat "requirements-dev.txt"
     - name: Install dependencies
       run: |

From a2feac32e2da0b1d255a88ce853ba94d8073958f Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+behxyz@users.noreply.github.com>
Date: Tue, 4 May 2021 07:11:57 -0400
Subject: [PATCH 13/14] Remove cucim mac only workaround

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>
---
 .github/workflows/pythonapp.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index f12e71273c..4ce068dd50 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -90,10 +90,6 @@ jobs:
         python -m pip install torch==1.8.1+cpu torchvision==0.9.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
         # min. requirements for windows instances
         python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines(txt[1:12]); f.close()"
-    - if: runner.os == 'macos'
-      name: Remove cucim installation (Mac only)
-      run: |
-        python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines([t for t in txt if not t.startswith('cucim')]); f.close()"
     - name: Install the dependencies
       run: |
         python -m pip install torch==1.8.1 torchvision==0.9.1

From c71698d644a7e5080c09f5f7e12b9dbd3fcd97e6 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+behxyz@users.noreply.github.com>
Date: Mon, 26 Jul 2021 15:56:57 +0000
Subject: [PATCH 14/14] Install cupy on only one cuda environment

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>
---
 .github/workflows/pythonapp.yml | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index 4ce068dd50..92a838d0a9 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -30,9 +30,6 @@ jobs:
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
-    - name: Remove CUDA-required dependencies
-      run: |
-        sed -i.bak -e "/^cupy/d" requirements-dev.txt
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip wheel
@@ -80,10 +77,6 @@ jobs:
       with:
         path: ${{ steps.pip-cache.outputs.dir }}
         key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
-    - if: runner.os != 'windows'
-      name: Remove CUDA-required dependencies (Mac and Linux)
-      run: |
-        sed -i.bak -e "/^cupy/d" requirements-dev.txt
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
@@ -278,10 +271,10 @@ jobs:
         python get-pip.py && \
         rm get-pip.py;
         fi
-    - name: Create the CUDA-dependent binary requirements for the environment
+    - if: matrix.environment == "PT18+CUDA112"
+      name: Add CuPy dependency to the latest CUDA environment
       run: |
-        sed -i.bak -e "s/cupy=/cupy-cuda$(echo ${{ matrix.environment }} | sed 's/^.*CUDA//')=/g" requirements-dev.txt
-        cat "requirements-dev.txt"
+        echo "cupy-cuda112" >> requirements-dev.txt
     - name: Install dependencies
       run: |
         which python