From 255a8994c48b4996878350f668e96e601c93e5c1 Mon Sep 17 00:00:00 2001 From: Lenz Fiedler Date: Sun, 2 Jun 2024 22:17:10 +0200 Subject: [PATCH 01/10] Added RODARE download --- .github/workflows/cpu-tests.yml | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/.github/workflows/cpu-tests.yml b/.github/workflows/cpu-tests.yml index 50c152bbb..c6fbf3f8e 100644 --- a/.github/workflows/cpu-tests.yml +++ b/.github/workflows/cpu-tests.yml @@ -171,13 +171,20 @@ jobs: # `requirements.txt` and/or extra dependencies are missing in the Docker Conda environment diff env_1.yml env_2.yml - - name: Check out repository (data) - uses: actions/checkout@v3 - with: - repository: mala-project/test-data - path: mala_data - ref: v1.7.0 - lfs: true + - name: Download test data repository + shell: 'bash -c "docker exec -i mala-cpu bash < {0}"' + run: | + # Download test data repository from RODARE. If the version changes + # this URL has to be adapted (the 29xx number and the version have + # to be incremented) + wget "https://rodare.hzdr.de/record/2901/files/mala-project/test-data-v1.7.4.zip" + + # Once downloaded, we have to unzip the file. The name of the root + # folder in the zip file has to be updated for data repository + # updates as well - the string at the end is the hash of the data + # repository commit. + unzip test-data-v1.7.4.zip + mv mala-project-test-data-a6458c5 mala_data - name: Test mala shell: 'bash -c "docker exec -i mala-cpu bash < {0}"' From 6289c808e45db92129b0442bb0663c3633c7a666 Mon Sep 17 00:00:00 2001 From: Lenz Fiedler Date: Sun, 2 Jun 2024 22:32:27 +0200 Subject: [PATCH 02/10] Adding unzip to the Dockerfile because it is needed for RODARE download --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 4350585ee..6ac48af50 100644 --- a/Dockerfile +++ b/Dockerfile @@ -8,6 +8,7 @@ RUN apt-get --allow-releaseinfo-change update && apt-get upgrade -y && \ libz-dev \ swig \ git-lfs \ + unzip \ cmake && \ apt-get clean && rm -rf /var/lib/apt/lists/* From e56fbe90852ad064b1ef11a3766b9825d74f41b9 Mon Sep 17 00:00:00 2001 From: Lenz Fiedler Date: Wed, 5 Jun 2024 09:31:32 +0200 Subject: [PATCH 03/10] Testing updating workflow --- .github/workflows/cpu-tests.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/cpu-tests.yml b/.github/workflows/cpu-tests.yml index c6fbf3f8e..af7b724f1 100644 --- a/.github/workflows/cpu-tests.yml +++ b/.github/workflows/cpu-tests.yml @@ -177,14 +177,14 @@ jobs: # Download test data repository from RODARE. If the version changes # this URL has to be adapted (the 29xx number and the version have # to be incremented) - wget "https://rodare.hzdr.de/record/2901/files/mala-project/test-data-v1.7.4.zip" + wget "https://rodare.hzdr.de/record/2996/files/mala-project/test-data-v1.7.7.zip" # Once downloaded, we have to unzip the file. The name of the root # folder in the zip file has to be updated for data repository # updates as well - the string at the end is the hash of the data # repository commit. - unzip test-data-v1.7.4.zip - mv mala-project-test-data-a6458c5 mala_data + unzip test-data-v1.7.7.zip + mv mala-project-test-data-bfb27c3 mala_data - name: Test mala shell: 'bash -c "docker exec -i mala-cpu bash < {0}"' From 9bc56537d2ad1716f3544a3b9e6940a8dc48e5ff Mon Sep 17 00:00:00 2001 From: Lenz Fiedler Date: Wed, 5 Jun 2024 09:43:59 +0200 Subject: [PATCH 04/10] Removed the LFS in data repo, this needs an update in the pipeline --- .github/workflows/cpu-tests.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/cpu-tests.yml b/.github/workflows/cpu-tests.yml index af7b724f1..9c6ccebc8 100644 --- a/.github/workflows/cpu-tests.yml +++ b/.github/workflows/cpu-tests.yml @@ -175,16 +175,16 @@ jobs: shell: 'bash -c "docker exec -i mala-cpu bash < {0}"' run: | # Download test data repository from RODARE. If the version changes - # this URL has to be adapted (the 29xx number and the version have - # to be incremented) - wget "https://rodare.hzdr.de/record/2996/files/mala-project/test-data-v1.7.7.zip" + # this URL has to be adapted (the number after /record/ and the + version have to be incremented) + wget "https://rodare.hzdr.de/record/2997/files/mala-project/test-data-v1.7.8.zip" # Once downloaded, we have to unzip the file. The name of the root # folder in the zip file has to be updated for data repository # updates as well - the string at the end is the hash of the data # repository commit. - unzip test-data-v1.7.7.zip - mv mala-project-test-data-bfb27c3 mala_data + unzip test-data-v1.7.8.zip + mv mala-project-test-data-46a6992 mala_data - name: Test mala shell: 'bash -c "docker exec -i mala-cpu bash < {0}"' From ccbcd6e04680cdc2089caf3c0cd6488b89a2dece Mon Sep 17 00:00:00 2001 From: Lenz Fiedler Date: Wed, 5 Jun 2024 09:59:55 +0200 Subject: [PATCH 05/10] Syntax error fixed --- .github/workflows/cpu-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/cpu-tests.yml b/.github/workflows/cpu-tests.yml index 9c6ccebc8..5d043e7fd 100644 --- a/.github/workflows/cpu-tests.yml +++ b/.github/workflows/cpu-tests.yml @@ -176,7 +176,7 @@ jobs: run: | # Download test data repository from RODARE. If the version changes # this URL has to be adapted (the number after /record/ and the - version have to be incremented) + # version have to be incremented) wget "https://rodare.hzdr.de/record/2997/files/mala-project/test-data-v1.7.8.zip" # Once downloaded, we have to unzip the file. The name of the root From 598d0216bb83c81ac8726d97bd389d768a2c81a4 Mon Sep 17 00:00:00 2001 From: Lenz Fiedler Date: Wed, 5 Jun 2024 10:24:20 +0200 Subject: [PATCH 06/10] Removed Git LFS from Docker and Docs --- Dockerfile | 1 - docs/source/install/installing_mala.rst | 6 +----- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/Dockerfile b/Dockerfile index 6ac48af50..79fc40a60 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,7 +7,6 @@ RUN apt-get --allow-releaseinfo-change update && apt-get upgrade -y && \ build-essential \ libz-dev \ swig \ - git-lfs \ unzip \ cmake && \ apt-get clean && rm -rf /var/lib/apt/lists/* diff --git a/docs/source/install/installing_mala.rst b/docs/source/install/installing_mala.rst index 9a46ed5b5..f34436ad4 100644 --- a/docs/source/install/installing_mala.rst +++ b/docs/source/install/installing_mala.rst @@ -37,17 +37,13 @@ The examples and tests need additional data to run. The MALA team provides a to check out the correct tag for the data repository, since the data repository itself is subject to ongoing development as well. -Also make sure to have the `Git LFS `_ installed on your -machine, since the data repository operates using Git LFS to handle large -binary files for example training data. - * Download data repository and check out correct tag: .. code-block:: bash git clone https://github.com/mala-project/test-data ~/path/to/data/repo cd ~/path/to/data/repo - git checkout v1.7.0 + git checkout v1.7.8 * Export the path to that repo by ``export MALA_DATA_REPO=~/path/to/data/repo`` From a85a280707c24b6feb5d093fd2d1118d5c7a7abc Mon Sep 17 00:00:00 2001 From: Lenz Fiedler <37868410+RandomDefaultUser@users.noreply.github.com> Date: Wed, 5 Jun 2024 16:54:38 +0200 Subject: [PATCH 07/10] Update Dockerfile Co-authored-by: Daniel Kotik --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 79fc40a60..724ed44e5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -8,6 +8,7 @@ RUN apt-get --allow-releaseinfo-change update && apt-get upgrade -y && \ libz-dev \ swig \ unzip \ + wget \ cmake && \ apt-get clean && rm -rf /var/lib/apt/lists/* From 8e84f2ec9466f558134864e40efa66979f503819 Mon Sep 17 00:00:00 2001 From: Lenz Fiedler <37868410+RandomDefaultUser@users.noreply.github.com> Date: Wed, 5 Jun 2024 16:54:58 +0200 Subject: [PATCH 08/10] Update .github/workflows/cpu-tests.yml Co-authored-by: Daniel Kotik --- .github/workflows/cpu-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/cpu-tests.yml b/.github/workflows/cpu-tests.yml index 5d043e7fd..1f3b52f40 100644 --- a/.github/workflows/cpu-tests.yml +++ b/.github/workflows/cpu-tests.yml @@ -183,7 +183,7 @@ jobs: # folder in the zip file has to be updated for data repository # updates as well - the string at the end is the hash of the data # repository commit. - unzip test-data-v1.7.8.zip + unzip -q test-data-v1.7.8.zip mv mala-project-test-data-46a6992 mala_data - name: Test mala From f013e84b90b60ba5312a6ffd055d56143d4418e9 Mon Sep 17 00:00:00 2001 From: Lenz Fiedler Date: Wed, 5 Jun 2024 17:19:48 +0200 Subject: [PATCH 09/10] Final version update --- .github/workflows/cpu-tests.yml | 6 +++--- docs/source/install/installing_mala.rst | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/cpu-tests.yml b/.github/workflows/cpu-tests.yml index 1f3b52f40..2d8c08895 100644 --- a/.github/workflows/cpu-tests.yml +++ b/.github/workflows/cpu-tests.yml @@ -177,14 +177,14 @@ jobs: # Download test data repository from RODARE. If the version changes # this URL has to be adapted (the number after /record/ and the # version have to be incremented) - wget "https://rodare.hzdr.de/record/2997/files/mala-project/test-data-v1.7.8.zip" + wget "https://rodare.hzdr.de/record/2999/files/mala-project/test-data-1.8.0.zip" # Once downloaded, we have to unzip the file. The name of the root # folder in the zip file has to be updated for data repository # updates as well - the string at the end is the hash of the data # repository commit. - unzip -q test-data-v1.7.8.zip - mv mala-project-test-data-46a6992 mala_data + unzip -q test-data-v1.8.0.zip + mv mala-project-test-data-d5694c7 mala_data - name: Test mala shell: 'bash -c "docker exec -i mala-cpu bash < {0}"' diff --git a/docs/source/install/installing_mala.rst b/docs/source/install/installing_mala.rst index f34436ad4..7ec2f25b9 100644 --- a/docs/source/install/installing_mala.rst +++ b/docs/source/install/installing_mala.rst @@ -43,7 +43,7 @@ itself is subject to ongoing development as well. git clone https://github.com/mala-project/test-data ~/path/to/data/repo cd ~/path/to/data/repo - git checkout v1.7.8 + git checkout v1.8.0 * Export the path to that repo by ``export MALA_DATA_REPO=~/path/to/data/repo`` From 0197a0ab9758db6d7aed0273163b486d307c0de5 Mon Sep 17 00:00:00 2001 From: Lenz Fiedler Date: Wed, 5 Jun 2024 17:33:09 +0200 Subject: [PATCH 10/10] Removed rogue "v" --- .github/workflows/cpu-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/cpu-tests.yml b/.github/workflows/cpu-tests.yml index 2d8c08895..1320e0cc9 100644 --- a/.github/workflows/cpu-tests.yml +++ b/.github/workflows/cpu-tests.yml @@ -183,7 +183,7 @@ jobs: # folder in the zip file has to be updated for data repository # updates as well - the string at the end is the hash of the data # repository commit. - unzip -q test-data-v1.8.0.zip + unzip -q test-data-1.8.0.zip mv mala-project-test-data-d5694c7 mala_data - name: Test mala