From 4d1f1d312cb03b96172cd0378097c2f13e05d503 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Mon, 28 Nov 2022 21:05:09 +0000 Subject: [PATCH 01/16] Try Python 3.10.6 --- build.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.json b/build.json index 868e56a1..86d11c1d 100644 --- a/build.json +++ b/build.json @@ -1,7 +1,7 @@ { "variable": { "PYTHON_VERSION": { - "default": "3.9.13" + "default": "3.10.6" }, "AIIDA_VERSION": { "default": "2.1.2" From 34d7e193d991e87408b7015e21223cd6af8a9b64 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Tue, 29 Nov 2022 14:14:41 +0000 Subject: [PATCH 02/16] Try fix aiidalab deps --- stack/lab/Dockerfile | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/stack/lab/Dockerfile b/stack/lab/Dockerfile index c05801d9..0d60354c 100644 --- a/stack/lab/Dockerfile +++ b/stack/lab/Dockerfile @@ -22,15 +22,17 @@ RUN apt-get update --yes && \ # Install aiidalab package ARG AIIDALAB_VERSION -RUN mamba install --yes \ - aiidalab=${AIIDALAB_VERSION} \ - && mamba clean --all -f -y && \ - fix-permissions "${CONDA_DIR}" && \ - fix-permissions "/home/${NB_USER}" +#RUN mamba install --yes \ +# aiidalab=${AIIDALAB_VERSION} \ +# && mamba clean --all -f -y && \ +# fix-permissions "${CONDA_DIR}" && \ +# fix-permissions "/home/${NB_USER}" +RUN git clone -b update-watchdog https://github.com/aiidalab/aiidalab.git && \ + cd aiidalab && pip install . # Pin aiidalab version. -RUN echo "aiidalab==${AIIDALAB_VERSION}" >> /opt/requirements.txt -RUN conda config --system --add pinned_packages "aiidalab=${AIIDALAB_VERSION}" +#RUN echo "aiidalab==${AIIDALAB_VERSION}" >> /opt/requirements.txt +#RUN conda config --system --add pinned_packages "aiidalab=${AIIDALAB_VERSION}" # Install the aiidalab-home app. ARG AIIDALAB_HOME_VERSION From 7dbdbaca90b580bdea2ccba956c2ef12c2d2ef5e Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Tue, 29 Nov 2022 15:04:43 +0000 Subject: [PATCH 03/16] Fix full-stack --- stack/full-stack/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile index 332454ff..f3701457 100644 --- a/stack/full-stack/Dockerfile +++ b/stack/full-stack/Dockerfile @@ -1,7 +1,7 @@ # syntax=docker/dockerfile:1 FROM base-with-services as base -FROM lab +FROM lab USER root @@ -10,7 +10,7 @@ COPY --from=base "${CONDA_DIR}/envs/aiida-core-services" "${CONDA_DIR}/envs/aiid COPY --from=base /usr/local/bin/before-notebook.d /usr/local/bin/before-notebook.d RUN fix-permissions "${CONDA_DIR}" -RUN fix-permissions "/home/${NB_USER}/.aiida" +RUN fix-permissions "/home/${NB_USER}" USER ${NB_USER} From 5bc9078a8437aa02416350771c192ec0b612fbfc Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Tue, 29 Nov 2022 15:28:06 +0000 Subject: [PATCH 04/16] Try 3.10.8 --- build.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.json b/build.json index 86d11c1d..02cd50ce 100644 --- a/build.json +++ b/build.json @@ -1,7 +1,7 @@ { "variable": { "PYTHON_VERSION": { - "default": "3.10.6" + "default": "3.10.8" }, "AIIDA_VERSION": { "default": "2.1.2" From ef5661bfbfc58c7c15ca7b208a9c0946cbf7ae7e Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Mon, 12 Dec 2022 14:58:03 +0000 Subject: [PATCH 05/16] Downgrade to Python 3.10.6 Not sure why the build started failing now. --- build.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.json b/build.json index 02cd50ce..86d11c1d 100644 --- a/build.json +++ b/build.json @@ -1,7 +1,7 @@ { "variable": { "PYTHON_VERSION": { - "default": "3.10.8" + "default": "3.10.6" }, "AIIDA_VERSION": { "default": "2.1.2" From 2111c72b6d8f06c28e9803164fb7afed2dd4ad75 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Fri, 17 Mar 2023 15:49:22 +0000 Subject: [PATCH 06/16] Revert aiidalab patch --- stack/lab/Dockerfile | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/stack/lab/Dockerfile b/stack/lab/Dockerfile index fe8e208b..feb132a2 100644 --- a/stack/lab/Dockerfile +++ b/stack/lab/Dockerfile @@ -23,17 +23,15 @@ RUN apt-get update --yes && \ # Install aiidalab package ARG AIIDALAB_VERSION -#RUN mamba install --yes \ -# aiidalab=${AIIDALAB_VERSION} \ -# && mamba clean --all -f -y && \ -# fix-permissions "${CONDA_DIR}" && \ -# fix-permissions "/home/${NB_USER}" -RUN git clone -b update-watchdog https://github.com/aiidalab/aiidalab.git && \ - cd aiidalab && pip install . +RUN mamba install --yes \ + aiidalab=${AIIDALAB_VERSION} \ + && mamba clean --all -f -y && \ + fix-permissions "${CONDA_DIR}" && \ + fix-permissions "/home/${NB_USER}" # Pin aiidalab version. -#RUN echo "aiidalab==${AIIDALAB_VERSION}" >> /opt/requirements.txt -#RUN conda config --system --add pinned_packages "aiidalab=${AIIDALAB_VERSION}" +RUN echo "aiidalab==${AIIDALAB_VERSION}" >> /opt/requirements.txt +RUN conda config --system --add pinned_packages "aiidalab=${AIIDALAB_VERSION}" # Install the aiidalab-home app. ARG AIIDALAB_HOME_VERSION From 480dcbd968dd202fa9e81927f79a7d3e74012086 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Mon, 20 Mar 2023 00:25:03 +0000 Subject: [PATCH 07/16] Python 3.10.8 --- build.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.json b/build.json index 8eff9abb..19b7301f 100644 --- a/build.json +++ b/build.json @@ -1,7 +1,7 @@ { "variable": { "PYTHON_VERSION": { - "default": "3.10.6" + "default": "3.10.8" }, "PGSQL_VERSION": { "default": "15" From ae4e87b45491309e97352740fa5c9ef1f8e46d82 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Mon, 20 Mar 2023 00:41:21 +0000 Subject: [PATCH 08/16] Python 3.10.9 --- build.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.json b/build.json index 19b7301f..c05b01df 100644 --- a/build.json +++ b/build.json @@ -1,7 +1,7 @@ { "variable": { "PYTHON_VERSION": { - "default": "3.10.8" + "default": "3.10.9" }, "PGSQL_VERSION": { "default": "15" From d9d24da2864ef541493cd76d95c8e1f872d55b0c Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Thu, 22 Jun 2023 21:54:48 +0100 Subject: [PATCH 09/16] Python 3.11.4 --- build.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.json b/build.json index e98e81a8..5eaac99b 100644 --- a/build.json +++ b/build.json @@ -1,7 +1,7 @@ { "variable": { "PYTHON_VERSION": { - "default": "3.10.9" + "default": "3.11.4" }, "PGSQL_VERSION": { "default": "15" From 071beb6d497a035118999515572dd62489dd2953 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Tue, 27 Jun 2023 14:28:43 +0100 Subject: [PATCH 10/16] Python 3.10.11 --- build.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.json b/build.json index 5eaac99b..4c38b2ad 100644 --- a/build.json +++ b/build.json @@ -1,7 +1,7 @@ { "variable": { "PYTHON_VERSION": { - "default": "3.11.4" + "default": "3.10.11" }, "PGSQL_VERSION": { "default": "15" From 8aabe32952d983d4dde634dcd9048376437e36eb Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Mon, 17 Jul 2023 16:59:07 +0100 Subject: [PATCH 11/16] Disable banner about Notebook v7 migration --- stack/lab/Dockerfile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/stack/lab/Dockerfile b/stack/lab/Dockerfile index 6c846483..84e3b054 100644 --- a/stack/lab/Dockerfile +++ b/stack/lab/Dockerfile @@ -82,7 +82,7 @@ WORKDIR "/home/${NB_USER}" RUN mkdir -p /home/${NB_USER}/apps -# When a Jupyter notebook server looses a connection to the frontend, +# NOTE 1: When a Jupyter notebook server looses a connection to the frontend, # it keeps the messages in a buffer. If there is a background thread running # and trying to update the frontend, the buffer grows indefinitely, # eventually consuming all available RAM. @@ -92,8 +92,10 @@ RUN mkdir -p /home/${NB_USER}/apps # but that may come with other problems for people with flaky internet connections. # Instead, here we configure Jupyter to kill all kernels that have been alive for # more than 12 hours. We also close all inactive terminals after 10 minutes. +# NOTE 2: show_banner=False disables the banner for upgrading to Notebook 7. ENV NOTEBOOK_ARGS \ "--NotebookApp.default_url='/apps/apps/home/start.ipynb'" \ + "--NotebookApp.show_banner=False" \ "--ContentsManager.allow_hidden=True" \ "--MappingKernelManager.buffer_offline_messages=True" \ "--MappingKernelManager.cull_busy=True" \ From e41bb60d8eae37b9696aca86fcf92bd830a17c0a Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Mon, 17 Jul 2023 17:07:37 +0100 Subject: [PATCH 12/16] DEBUG: Do not upgrade pip before installing dev dependencies --- .github/actions/create-dev-env/action.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/actions/create-dev-env/action.yml b/.github/actions/create-dev-env/action.yml index 169d8bcb..b5e46326 100644 --- a/.github/actions/create-dev-env/action.yml +++ b/.github/actions/create-dev-env/action.yml @@ -22,6 +22,5 @@ runs: - name: Install Dev Dependencies 📦 run: | - pip install --upgrade pip pip install --upgrade -r requirements-dev.txt shell: bash From 730c73eec8da79d01d2601501ebd3cffffc6d50e Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Mon, 17 Jul 2023 18:24:43 +0100 Subject: [PATCH 13/16] Revert "DEBUG: Do not upgrade pip before installing dev dependencies" This reverts commit e41bb60d8eae37b9696aca86fcf92bd830a17c0a. --- .github/actions/create-dev-env/action.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/actions/create-dev-env/action.yml b/.github/actions/create-dev-env/action.yml index b5e46326..169d8bcb 100644 --- a/.github/actions/create-dev-env/action.yml +++ b/.github/actions/create-dev-env/action.yml @@ -22,5 +22,6 @@ runs: - name: Install Dev Dependencies 📦 run: | + pip install --upgrade pip pip install --upgrade -r requirements-dev.txt shell: bash From 5ab51dcb2d42c53a84c7985ecacb58c04dfa644c Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Mon, 17 Jul 2023 18:25:20 +0100 Subject: [PATCH 14/16] Pin PyYAML<=5.3 https://github.com/yaml/pyyaml/issues/601#issuecomment-1638555590 --- requirements-dev.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements-dev.txt b/requirements-dev.txt index 7381a21c..458c829c 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -12,3 +12,4 @@ pytest-docker docker-compose doit dunamai +pyyaml<=5.3.1 From 33946f60030d0e4fdf4966611809597554cdc61a Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Mon, 17 Jul 2023 19:03:01 +0100 Subject: [PATCH 15/16] Disable tests temporarily --- .github/workflows/docker-build-test-upload.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docker-build-test-upload.yml b/.github/workflows/docker-build-test-upload.yml index 39d5bb88..94d1692b 100644 --- a/.github/workflows/docker-build-test-upload.yml +++ b/.github/workflows/docker-build-test-upload.yml @@ -39,9 +39,9 @@ jobs: BUILDKIT_PROGRESS: plain shell: bash - - name: Run tests ✅ - run: VERSION=newly-build pytest -s tests/test-common.py tests/test-${{ inputs.image }}.py --variant ${{ inputs.image }} - shell: bash + # - name: Run tests ✅ + #run: VERSION=newly-build pytest -s tests/test-common.py tests/test-${{ inputs.image }}.py --variant ${{ inputs.image }} + #shell: bash - name: Save image as a tar for later use 💾 run: docker save ${{ env.OWNER }}/${{ inputs.image }} -o /tmp/${{ inputs.image }}-${{ inputs.architecture }}.tar From 161dbae86d72bf82fb335c5a7497ba36f2f142d1 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Tue, 18 Jul 2023 16:27:56 +0100 Subject: [PATCH 16/16] Revert "Disable tests temporarily" This reverts commit 33946f60030d0e4fdf4966611809597554cdc61a. --- .github/workflows/docker-build-test-upload.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docker-build-test-upload.yml b/.github/workflows/docker-build-test-upload.yml index 94d1692b..39d5bb88 100644 --- a/.github/workflows/docker-build-test-upload.yml +++ b/.github/workflows/docker-build-test-upload.yml @@ -39,9 +39,9 @@ jobs: BUILDKIT_PROGRESS: plain shell: bash - # - name: Run tests ✅ - #run: VERSION=newly-build pytest -s tests/test-common.py tests/test-${{ inputs.image }}.py --variant ${{ inputs.image }} - #shell: bash + - name: Run tests ✅ + run: VERSION=newly-build pytest -s tests/test-common.py tests/test-${{ inputs.image }}.py --variant ${{ inputs.image }} + shell: bash - name: Save image as a tar for later use 💾 run: docker save ${{ env.OWNER }}/${{ inputs.image }} -o /tmp/${{ inputs.image }}-${{ inputs.architecture }}.tar