From c82bd9078f39c19de1f856f958cf6af6df10fa58 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 11 May 2023 15:56:17 +0100
Subject: [PATCH 01/14] Create publish_map.yml

---
 .github/workflows/publish_map.yml | 43 +++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 .github/workflows/publish_map.yml

diff --git a/.github/workflows/publish_map.yml b/.github/workflows/publish_map.yml
new file mode 100644
index 0000000..00e2acc
--- /dev/null
+++ b/.github/workflows/publish_map.yml
@@ -0,0 +1,43 @@
+# Workflow to publish TotalSegmentator-AIDE MAP on GHCR
+
+name: Create and publish MAP
+
+on:
+  push:
+    branches: ['24_publish_map']
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
\ No newline at end of file

From 3a86f16a409daae4b49d5d401c3012ec65f08a23 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 11 May 2023 16:43:02 +0100
Subject: [PATCH 02/14] Change to build and package MAP using command line

---
 .github/workflows/publish_map.yml | 76 +++++++++++++++++--------------
 1 file changed, 43 insertions(+), 33 deletions(-)

diff --git a/.github/workflows/publish_map.yml b/.github/workflows/publish_map.yml
index 00e2acc..951aae7 100644
--- a/.github/workflows/publish_map.yml
+++ b/.github/workflows/publish_map.yml
@@ -1,43 +1,53 @@
 # Workflow to publish TotalSegmentator-AIDE MAP on GHCR
 
-name: Create and publish MAP
+name: Build and package MAP
 
 on:
   push:
     branches: ['24_publish_map']
 
-env:
-  REGISTRY: ghcr.io
-  IMAGE_NAME: ${{ github.repository }}
-
 jobs:
-  build-and-push-image:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: write
+  build:
+
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest ]
+        python-version: [ '3.10' ]
+
+    defaults:
+      run:
+        shell: bash -l {0}
 
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v3
-
-      - name: Log in to the Container registry
-        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
-        with:
-          registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Extract metadata (tags, labels) for Docker
-        id: meta
-        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
-        with:
-          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-
-      - name: Build and push Docker image
-        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
-        with:
-          context: .
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
\ No newline at end of file
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install Python packages
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest pytest-cov
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+    - name: Display installed pip packages
+      run: |
+        pip list
+
+    - name: Initial packaging of MAP-init
+      run: |
+        monai-deploy package app --tag map-init -l DEBUG
+
+    - name: Package 3rd-party software into MAP
+      run: |
+        docker build -t map app/
+
+#    # TODO: add step to run the MAP using test data
+#    - name: Test MAP end-to-end
+#      run: |
+#        monai-deploy run map input-test-data-in-repo/ output/
\ No newline at end of file

From b214bc45e8d667d8b70e7852850bfdb2dc8a113c Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Fri, 12 May 2023 13:50:46 +0100
Subject: [PATCH 03/14] Updates GitHub Action to use map-init in build process
 / adds output file check

---
 .github/workflows/publish_map.yml | 14 +++++++++-----
 app/Dockerfile                    |  4 +++-
 tests/data/output/.gitkeep        |  0
 3 files changed, 12 insertions(+), 6 deletions(-)
 create mode 100644 tests/data/output/.gitkeep

diff --git a/.github/workflows/publish_map.yml b/.github/workflows/publish_map.yml
index 951aae7..cc26c84 100644
--- a/.github/workflows/publish_map.yml
+++ b/.github/workflows/publish_map.yml
@@ -45,9 +45,13 @@ jobs:
 
     - name: Package 3rd-party software into MAP
       run: |
-        docker build -t map app/
+        docker build --build-arg INIT_CONTAINER=map-init -t map app
 
-#    # TODO: add step to run the MAP using test data
-#    - name: Test MAP end-to-end
-#      run: |
-#        monai-deploy run map input-test-data-in-repo/ output/
\ No newline at end of file
+    - name: Test MAP end-to-end
+      run: |
+        monai-deploy run map tests/data/rtstructwriter/dcm tests/data/output
+
+    - name: Confirm output generated
+      run: |
+        ls tests/data/output
+        if test -f "tests/data/output/output-rt-struct.dcm"; then echo "Output RT Struct exists."; fi
\ No newline at end of file
diff --git a/app/Dockerfile b/app/Dockerfile
index 1a270e4..71a7b71 100644
--- a/app/Dockerfile
+++ b/app/Dockerfile
@@ -1,5 +1,7 @@
+ARG INIT_CONTAINER
+
 # Use initial MAP for build
-FROM ghcr.io/gstt-csc/totalsegmentator-aide/map-init:0.1.2 AS build
+FROM $INIT_CONTAINER AS build
 
 # Add dcm2niix to MAP
 WORKDIR /bin
diff --git a/tests/data/output/.gitkeep b/tests/data/output/.gitkeep
new file mode 100644
index 0000000..e69de29

From 8ff68eb2122e547d3ed3a38aa76c3a2b9a2156b1 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Fri, 12 May 2023 14:51:04 +0100
Subject: [PATCH 04/14] Test GitHub Action with updated Docker image name

---
 .github/workflows/publish_map.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/publish_map.yml b/.github/workflows/publish_map.yml
index cc26c84..cad78a5 100644
--- a/.github/workflows/publish_map.yml
+++ b/.github/workflows/publish_map.yml
@@ -41,11 +41,15 @@ jobs:
 
     - name: Initial packaging of MAP-init
       run: |
-        monai-deploy package app --tag map-init -l DEBUG
+        monai-deploy package app --tag map/init:temp -l DEBUG
 
     - name: Package 3rd-party software into MAP
       run: |
-        docker build --build-arg INIT_CONTAINER=map-init -t map app
+        docker build --build-arg INIT_CONTAINER=map-init -t map/final:temp app
+
+    - name: Show Docker images
+      run: |
+        docker images
 
     - name: Test MAP end-to-end
       run: |

From d4f53fc616bc819a67a117a34dbb22370e2408cd Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Fri, 12 May 2023 15:21:52 +0100
Subject: [PATCH 05/14] =?UTF-8?q?Typo=20=E2=80=93=20re-test=20GHA?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

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

diff --git a/.github/workflows/publish_map.yml b/.github/workflows/publish_map.yml
index cad78a5..d2ab8e9 100644
--- a/.github/workflows/publish_map.yml
+++ b/.github/workflows/publish_map.yml
@@ -45,7 +45,7 @@ jobs:
 
     - name: Package 3rd-party software into MAP
       run: |
-        docker build --build-arg INIT_CONTAINER=map-init -t map/final:temp app
+        docker build --build-arg INIT_CONTAINER=map/init:temp -t map/final:temp app
 
     - name: Show Docker images
       run: |

From 963706fc636a88c2a820195bbf78ca9d84047dc8 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 30 May 2023 11:56:15 +0100
Subject: [PATCH 06/14] WIP: test publish_map.yml using one step for all MAP
 commands

---
 .github/workflows/publish_map.yml | 15 ++-------------
 1 file changed, 2 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/publish_map.yml b/.github/workflows/publish_map.yml
index d2ab8e9..e836b5d 100644
--- a/.github/workflows/publish_map.yml
+++ b/.github/workflows/publish_map.yml
@@ -39,23 +39,12 @@ jobs:
       run: |
         pip list
 
-    - name: Initial packaging of MAP-init
+    - name: Package MAP & test MAP end-to-end
       run: |
         monai-deploy package app --tag map/init:temp -l DEBUG
-
-    - name: Package 3rd-party software into MAP
-      run: |
+        docker images
         docker build --build-arg INIT_CONTAINER=map/init:temp -t map/final:temp app
-
-    - name: Show Docker images
-      run: |
         docker images
-
-    - name: Test MAP end-to-end
-      run: |
         monai-deploy run map tests/data/rtstructwriter/dcm tests/data/output
-
-    - name: Confirm output generated
-      run: |
         ls tests/data/output
         if test -f "tests/data/output/output-rt-struct.dcm"; then echo "Output RT Struct exists."; fi
\ No newline at end of file

From 1f201dc92bd281be6a5eb66e85039f1647ed4f08 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Wed, 5 Jul 2023 14:16:14 +0100
Subject: [PATCH 07/14] Test GHA with 22.08 Nvidia PyTorch base image

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

diff --git a/.github/workflows/publish_map.yml b/.github/workflows/publish_map.yml
index e836b5d..faed7e3 100644
--- a/.github/workflows/publish_map.yml
+++ b/.github/workflows/publish_map.yml
@@ -41,7 +41,7 @@ jobs:
 
     - name: Package MAP & test MAP end-to-end
       run: |
-        monai-deploy package app --tag map/init:temp -l DEBUG
+        monai-deploy package app --base nvcr.io/nvidia/pytorch:22.08-py3 --tag map/init:temp -l DEBUG
         docker images
         docker build --build-arg INIT_CONTAINER=map/init:temp -t map/final:temp app
         docker images

From 6f35dd89ddfe46433fbf3802ee568f5cb2ac33c6 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Wed, 5 Jul 2023 16:07:06 +0100
Subject: [PATCH 08/14] Test monai-deploy package with custom -r flag

Use requirements-map-init.txt to force Python package versions compatible with scipy==1.6.3 which is default version in Nvidia PyTorch containers.

Alternatively, could use -r flag to install newer version of scipy.
---
 .github/workflows/publish_map.yml | 2 +-
 requirements-map-init.txt         | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)
 create mode 100644 requirements-map-init.txt

diff --git a/.github/workflows/publish_map.yml b/.github/workflows/publish_map.yml
index faed7e3..bb14d99 100644
--- a/.github/workflows/publish_map.yml
+++ b/.github/workflows/publish_map.yml
@@ -41,7 +41,7 @@ jobs:
 
     - name: Package MAP & test MAP end-to-end
       run: |
-        monai-deploy package app --base nvcr.io/nvidia/pytorch:22.08-py3 --tag map/init:temp -l DEBUG
+        monai-deploy package app --base nvcr.io/nvidia/pytorch:22.08-py3 -r requirements-map-init.txt --tag map/init:temp -l DEBUG
         docker images
         docker build --build-arg INIT_CONTAINER=map/init:temp -t map/final:temp app
         docker images
diff --git a/requirements-map-init.txt b/requirements-map-init.txt
new file mode 100644
index 0000000..50ad4e7
--- /dev/null
+++ b/requirements-map-init.txt
@@ -0,0 +1,2 @@
+numpy<1.21.0
+protobuf<3.20
\ No newline at end of file

From 6aa53aad2b85056d740accdab2e9b493996ed0ea Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Fri, 7 Jul 2023 11:08:02 +0100
Subject: [PATCH 09/14] Test GHA: adds in free disk space step

---
 .github/workflows/publish_map.yml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.github/workflows/publish_map.yml b/.github/workflows/publish_map.yml
index bb14d99..e6e5f60 100644
--- a/.github/workflows/publish_map.yml
+++ b/.github/workflows/publish_map.yml
@@ -39,6 +39,15 @@ jobs:
       run: |
         pip list
 
+    - name: Free disk space
+      run: |
+        df -h
+        sudo swapoff -a
+        sudo rm -rf /swapfile /usr/share/dotnet /usr/local/lib/android /opt/ghc
+        sudo apt clean
+        docker rmi $(docker image ls -aq)
+        df -h
+
     - name: Package MAP & test MAP end-to-end
       run: |
         monai-deploy package app --base nvcr.io/nvidia/pytorch:22.08-py3 -r requirements-map-init.txt --tag map/init:temp -l DEBUG

From fc91ab30a604229a0f01682eae04e8a4783ed68d Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Fri, 7 Jul 2023 11:53:09 +0100
Subject: [PATCH 10/14] Test GHA: adds --working-dir option and remove slashes
 from image names

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

diff --git a/.github/workflows/publish_map.yml b/.github/workflows/publish_map.yml
index e6e5f60..2a91710 100644
--- a/.github/workflows/publish_map.yml
+++ b/.github/workflows/publish_map.yml
@@ -50,9 +50,9 @@ jobs:
 
     - name: Package MAP & test MAP end-to-end
       run: |
-        monai-deploy package app --base nvcr.io/nvidia/pytorch:22.08-py3 -r requirements-map-init.txt --tag map/init:temp -l DEBUG
+        monai-deploy package app --base nvcr.io/nvidia/pytorch:22.08-py3 -r requirements-map-init.txt --working-dir app --tag map-init:temp -l DEBUG
         docker images
-        docker build --build-arg INIT_CONTAINER=map/init:temp -t map/final:temp app
+        docker build --build-arg INIT_CONTAINER=map-init:temp -t map-final:temp app
         docker images
         monai-deploy run map tests/data/rtstructwriter/dcm tests/data/output
         ls tests/data/output

From bae5cc797951861d45a82aaff9bb8f81027bcad4 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Fri, 7 Jul 2023 12:59:13 +0100
Subject: [PATCH 11/14] Test GHA: specify requirements.txt via md decorator

---
 .github/workflows/publish_map.yml | 2 +-
 app/app.py                        | 6 ++++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/publish_map.yml b/.github/workflows/publish_map.yml
index 2a91710..9a44e78 100644
--- a/.github/workflows/publish_map.yml
+++ b/.github/workflows/publish_map.yml
@@ -50,7 +50,7 @@ jobs:
 
     - name: Package MAP & test MAP end-to-end
       run: |
-        monai-deploy package app --base nvcr.io/nvidia/pytorch:22.08-py3 -r requirements-map-init.txt --working-dir app --tag map-init:temp -l DEBUG
+        monai-deploy package app --base nvcr.io/nvidia/pytorch:22.08-py3 --tag map-init:temp -l DEBUG
         docker images
         docker build --build-arg INIT_CONTAINER=map-init:temp -t map-final:temp app
         docker images
diff --git a/app/app.py b/app/app.py
index be6f9cf..26662fc 100644
--- a/app/app.py
+++ b/app/app.py
@@ -9,15 +9,21 @@
 # Tom Roberts (tom.roberts@gstt.nhs.uk / t.roberts@kcl.ac.uk)
 
 import logging
+from pathlib import Path
 
+import monai.deploy.core as md
 from monai.deploy.core import Application, resource
 
 from operators.dcm2nii_operator import Dcm2NiiOperator
 from operators.rtstructwriter_operator import RTStructWriterOperator
 from operators.totalsegmentator_operator import TotalSegmentatorOperator
 
+requirements_file = (
+    Path(__file__).resolve().parent / ".." / "requirements.txt"
+)
 
 @resource(cpu=1, gpu=1, memory="32Gi")
+@md.env(pip_packages=requirements_file.as_posix())
 class TotalSegmentatorApp(Application):
     """
     TotalSegmentator - segmentation of 104 anatomical structures in CT images.

From 98b7c07f80c795e86be2162c0f38777c6aaf82c4 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Fri, 7 Jul 2023 13:28:05 +0100
Subject: [PATCH 12/14] Test GHA: create app_requirements.txt within app/ dir

---
 app/app.py               |  2 +-
 app/app_requirements.txt | 68 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 69 insertions(+), 1 deletion(-)
 create mode 100644 app/app_requirements.txt

diff --git a/app/app.py b/app/app.py
index 26662fc..14f0055 100644
--- a/app/app.py
+++ b/app/app.py
@@ -19,7 +19,7 @@
 from operators.totalsegmentator_operator import TotalSegmentatorOperator
 
 requirements_file = (
-    Path(__file__).resolve().parent / ".." / "requirements.txt"
+    Path(__file__).resolve().parent / "app_requirements.txt"
 )
 
 @resource(cpu=1, gpu=1, memory="32Gi")
diff --git a/app/app_requirements.txt b/app/app_requirements.txt
new file mode 100644
index 0000000..1ac94ed
--- /dev/null
+++ b/app/app_requirements.txt
@@ -0,0 +1,68 @@
+aiohttp==3.8.3
+aiosignal==1.3.1
+async-timeout==4.0.2
+attrs==22.2.0
+batchgenerators==0.21
+certifi==2022.12.7
+charset-normalizer==2.1.1
+colorama==0.4.6
+contourpy==1.0.6
+cycler==0.11.0
+dataclasses==0.6
+dicom2nifti==2.4.7
+dill==0.3.6
+fonttools==4.38.0
+frozenlist==1.3.3
+fury==0.8.0
+future==0.18.3
+idna==3.4
+imageio==2.23.0
+joblib==1.2.0
+kiwisolver==1.4.4
+linecache2==1.0.0
+matplotlib==3.6.2
+MedPy==0.4.0
+monai-deploy-app-sdk==0.5.0
+multidict==6.0.4
+multiprocess==0.70.14
+networkx==2.8.8
+nibabel==4.0.2
+nnunet-customized==1.2
+numpy==1.24.1
+opencv-python==4.7.0.68
+p-tqdm==1.4.0
+packaging==22.0
+pandas==1.5.2
+pathos==0.3.0
+Pillow==9.3.0
+pox==0.3.2
+ppft==1.7.6.6
+psutil==5.9.4
+pydicom==2.3.1
+pytest==7.2.1
+pyparsing==3.0.9
+python-dateutil==2.8.2
+python-gdcm==3.0.20
+pytz==2022.7
+PyWavelets==1.4.1
+requests==2.28.1
+rt-utils==1.2.7
+scikit-image==0.19.3
+scikit-learn==1.2.0
+scipy==1.9.3
+SimpleITK==2.2.1
+six==1.16.0
+threadpoolctl==3.1.0
+tifffile==2022.10.10
+torch==1.13.1
+TotalSegmentator==1.5.5
+tqdm==4.64.1
+traceback2==1.4.0
+typeguard==2.13.3
+typing_extensions==4.4.0
+unittest2==1.1.0
+urllib3==1.26.13
+vtk==9.2.2
+wslink==1.10.0
+xvfbwrapper==0.2.9
+yarl==1.8.2

From 4a31b0c4a0000cfeb2bff1b77896f142b32e8690 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Fri, 7 Jul 2023 13:52:13 +0100
Subject: [PATCH 13/14] Test GHA: pip Python packages without specifying
 versions

---
 app/app_requirements.txt | 75 ++++------------------------------------
 1 file changed, 7 insertions(+), 68 deletions(-)

diff --git a/app/app_requirements.txt b/app/app_requirements.txt
index 1ac94ed..949c349 100644
--- a/app/app_requirements.txt
+++ b/app/app_requirements.txt
@@ -1,68 +1,7 @@
-aiohttp==3.8.3
-aiosignal==1.3.1
-async-timeout==4.0.2
-attrs==22.2.0
-batchgenerators==0.21
-certifi==2022.12.7
-charset-normalizer==2.1.1
-colorama==0.4.6
-contourpy==1.0.6
-cycler==0.11.0
-dataclasses==0.6
-dicom2nifti==2.4.7
-dill==0.3.6
-fonttools==4.38.0
-frozenlist==1.3.3
-fury==0.8.0
-future==0.18.3
-idna==3.4
-imageio==2.23.0
-joblib==1.2.0
-kiwisolver==1.4.4
-linecache2==1.0.0
-matplotlib==3.6.2
-MedPy==0.4.0
-monai-deploy-app-sdk==0.5.0
-multidict==6.0.4
-multiprocess==0.70.14
-networkx==2.8.8
-nibabel==4.0.2
-nnunet-customized==1.2
-numpy==1.24.1
-opencv-python==4.7.0.68
-p-tqdm==1.4.0
-packaging==22.0
-pandas==1.5.2
-pathos==0.3.0
-Pillow==9.3.0
-pox==0.3.2
-ppft==1.7.6.6
-psutil==5.9.4
-pydicom==2.3.1
-pytest==7.2.1
-pyparsing==3.0.9
-python-dateutil==2.8.2
-python-gdcm==3.0.20
-pytz==2022.7
-PyWavelets==1.4.1
-requests==2.28.1
-rt-utils==1.2.7
-scikit-image==0.19.3
-scikit-learn==1.2.0
-scipy==1.9.3
-SimpleITK==2.2.1
-six==1.16.0
-threadpoolctl==3.1.0
-tifffile==2022.10.10
-torch==1.13.1
-TotalSegmentator==1.5.5
-tqdm==4.64.1
-traceback2==1.4.0
-typeguard==2.13.3
-typing_extensions==4.4.0
-unittest2==1.1.0
-urllib3==1.26.13
-vtk==9.2.2
-wslink==1.10.0
-xvfbwrapper==0.2.9
-yarl==1.8.2
+torch
+monai-deploy-app-sdk
+highdicom
+nibabel
+monai
+rt_utils
+typeguard~=2.12.1  # known issue in monai-deploy-app-sdk https://github.com/Project-MONAI/monai-deploy-app-sdk/issues/410

From 56f6074dd8bd666a7152e7ef827b2087506573de Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Fri, 7 Jul 2023 14:56:00 +0100
Subject: [PATCH 14/14] Test GHA: only pip install app_requirements.txt

i.e. minimal amount of packages
---
 .github/workflows/publish_map.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/publish_map.yml b/.github/workflows/publish_map.yml
index 9a44e78..5fc67d6 100644
--- a/.github/workflows/publish_map.yml
+++ b/.github/workflows/publish_map.yml
@@ -33,7 +33,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install flake8 pytest pytest-cov
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install -r app/app_requirements.txt
 
     - name: Display installed pip packages
       run: |