From d62a24b0eb5e01be37261f1c28eec4d86002fed4 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Tue, 14 May 2024 01:10:58 +0100 Subject: [PATCH 01/20] Update base image to python-3.10.11 --- build.json | 2 +- stack/full-stack/Dockerfile | 2 +- stack/lab/Dockerfile | 4 +++- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/build.json b/build.json index 99339785..2f906b75 100644 --- a/build.json +++ b/build.json @@ -1,7 +1,7 @@ { "variable": { "PYTHON_VERSION": { - "default": "3.9.13" + "default": "3.10.11" }, "PGSQL_VERSION": { "default": "15" diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile index 61ea23a5..cebeb532 100644 --- a/stack/full-stack/Dockerfile +++ b/stack/full-stack/Dockerfile @@ -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 ${NB_USER} diff --git a/stack/lab/Dockerfile b/stack/lab/Dockerfile index 3bcb97bd..0c2d29cd 100644 --- a/stack/lab/Dockerfile +++ b/stack/lab/Dockerfile @@ -77,7 +77,7 @@ WORKDIR "/home/${NB_USER}" RUN mkdir -p /home/${NB_USER}/apps -# When a Jupyter notebook server looses a connection to the frontend, +# NOTE1: When a Jupyter notebook server looses a connection to the frontend, # it keeps the messages in a buffer. If there is a background thread running # and trying to update the frontend, the buffer grows indefinitely, # eventually consuming all available RAM. @@ -87,8 +87,10 @@ RUN mkdir -p /home/${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. +# NOTE2: 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 e52ca1e032a3717abbd53699d18bd427ad091702 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Jun 2024 02:23:27 +0200 Subject: [PATCH 02/20] 3.11.3 --- build.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.json b/build.json index 2f906b75..9661e6b3 100644 --- a/build.json +++ b/build.json @@ -1,7 +1,7 @@ { "variable": { "PYTHON_VERSION": { - "default": "3.10.11" + "default": "3.11.3" }, "PGSQL_VERSION": { "default": "15" From 4a77ab983b0d89249641a5bdc4516e2721387809 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Thu, 20 Jun 2024 21:47:56 +0200 Subject: [PATCH 03/20] Update mamba --- stack/base/Dockerfile | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/stack/base/Dockerfile b/stack/base/Dockerfile index 08e625ab..b5e6d033 100644 --- a/stack/base/Dockerfile +++ b/stack/base/Dockerfile @@ -44,11 +44,10 @@ ENV PIP_CONSTRAINT /opt/requirements.txt # Ensure that pip installs packages to ~/.local by default ENV PIP_USER 1 -# Upgrade pip to latest -RUN mamba update -y pip && mamba clean --all -f -y - +# Upgrade pip and mamba to latest # Install aiida-core and other shared requirements. -RUN mamba install --yes \ +RUN mamba update -y pip mamba && \ + mamba install --yes \ aiida-core==${AIIDA_VERSION} \ mamba-bash-completion \ && mamba clean --all -f -y && \ From 4985362bc7149486bca380d94c53886e9dc56fe9 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Thu, 20 Jun 2024 22:13:47 +0200 Subject: [PATCH 04/20] Update zstandard --- stack/base/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stack/base/Dockerfile b/stack/base/Dockerfile index b5e6d033..fe54d2dc 100644 --- a/stack/base/Dockerfile +++ b/stack/base/Dockerfile @@ -46,7 +46,7 @@ ENV PIP_USER 1 # Upgrade pip and mamba to latest # Install aiida-core and other shared requirements. -RUN mamba update -y pip mamba && \ +RUN mamba update -y pip mamba zstandard && \ mamba install --yes \ aiida-core==${AIIDA_VERSION} \ mamba-bash-completion \ From 5ce75da8613e4d1bb80d5377d8c26ac60b6aac29 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Fri, 21 Jun 2024 12:37:39 +0200 Subject: [PATCH 05/20] Install aiidalab from git --- stack/lab/Dockerfile | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/stack/lab/Dockerfile b/stack/lab/Dockerfile index 0c2d29cd..5f0f8ed1 100644 --- a/stack/lab/Dockerfile +++ b/stack/lab/Dockerfile @@ -15,11 +15,12 @@ WORKDIR /opt/ # 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/${NB_USER}" +RUN pip install --no-user aiidalab@git+https://github.com/aiidalab/aiidalab.git +#RUN mamba install --yes \ +# aiidalab=${AIIDALAB_VERSION} \ +# && mamba clean --all -f -y && \ +# fix-permissions "${CONDA_DIR}" && \ +# fix-permissions "/home/${NB_USER}" # Pin aiidalab version. RUN echo "aiidalab==${AIIDALAB_VERSION}" >> /opt/requirements.txt From dd63d3bbe4d4bd21367f21945353f0d2dc4f9e6c Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 22 Jun 2024 06:03:21 +0200 Subject: [PATCH 06/20] Update stack/base/Dockerfile --- stack/base/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stack/base/Dockerfile b/stack/base/Dockerfile index fe54d2dc..f3af9f1e 100644 --- a/stack/base/Dockerfile +++ b/stack/base/Dockerfile @@ -46,7 +46,7 @@ ENV PIP_USER 1 # Upgrade pip and mamba to latest # Install aiida-core and other shared requirements. -RUN mamba update -y pip mamba zstandard && \ +RUN mamba update -y pip zstandard && \ mamba install --yes \ aiida-core==${AIIDA_VERSION} \ mamba-bash-completion \ From 3fe3513e90b70d354caf4ded74fbdf570d263b7a Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 22 Jun 2024 18:57:37 +0200 Subject: [PATCH 07/20] Install aiidalab from fork --- stack/lab/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stack/lab/Dockerfile b/stack/lab/Dockerfile index 5f0f8ed1..7bb6ac0b 100644 --- a/stack/lab/Dockerfile +++ b/stack/lab/Dockerfile @@ -15,7 +15,7 @@ WORKDIR /opt/ # Install aiidalab package ARG AIIDALAB_VERSION -RUN pip install --no-user aiidalab@git+https://github.com/aiidalab/aiidalab.git +RUN pip install --no-user aiidalab@git+https://github.com/aiidalab/aiidalab #RUN mamba install --yes \ # aiidalab=${AIIDALAB_VERSION} \ # && mamba clean --all -f -y && \ From 3f28b84500e36ff04aab81327f9093d45154f114 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sun, 7 Jul 2024 16:23:12 +0100 Subject: [PATCH 08/20] Bump aiidalab to 24.07.0 --- build.json | 2 +- stack/lab/Dockerfile | 11 +++++------ 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/build.json b/build.json index 9661e6b3..610c96da 100644 --- a/build.json +++ b/build.json @@ -13,7 +13,7 @@ "default": "2.5.1" }, "AIIDALAB_VERSION": { - "default": "23.03.2" + "default": "24.07.0" }, "AIIDALAB_HOME_VERSION": { "default": "23.03.1" diff --git a/stack/lab/Dockerfile b/stack/lab/Dockerfile index 7bb6ac0b..0c2d29cd 100644 --- a/stack/lab/Dockerfile +++ b/stack/lab/Dockerfile @@ -15,12 +15,11 @@ WORKDIR /opt/ # Install aiidalab package ARG AIIDALAB_VERSION -RUN pip install --no-user aiidalab@git+https://github.com/aiidalab/aiidalab -#RUN mamba install --yes \ -# aiidalab=${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/${NB_USER}" # Pin aiidalab version. RUN echo "aiidalab==${AIIDALAB_VERSION}" >> /opt/requirements.txt From fcceb68aa65508382d0b6af4b1baf338d15bf0e9 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sun, 7 Jul 2024 16:51:54 +0100 Subject: [PATCH 09/20] Fix aiidalab version --- build.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.json b/build.json index 610c96da..7cf17043 100644 --- a/build.json +++ b/build.json @@ -13,7 +13,7 @@ "default": "2.5.1" }, "AIIDALAB_VERSION": { - "default": "24.07.0" + "default": "24.7.0" }, "AIIDALAB_HOME_VERSION": { "default": "23.03.1" From 5ae2e645727fbf1739a440e4f345b02ef963aa5c Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Fri, 6 Sep 2024 13:07:26 +0100 Subject: [PATCH 10/20] Remove traitlets install --- stack/base/Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/stack/base/Dockerfile b/stack/base/Dockerfile index bb41cb28..fb772ba7 100644 --- a/stack/base/Dockerfile +++ b/stack/base/Dockerfile @@ -52,7 +52,6 @@ RUN mamba update -y pip zstandard async_generator certipy && \ mamba install --yes \ aiida-core==${AIIDA_VERSION} \ mamba-bash-completion \ - traitlets=5.9.0 \ && mamba clean --all -f -y && \ fix-permissions "${CONDA_DIR}" From d42e04ced776267a689f596f9b6d525ccac69158 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sun, 8 Sep 2024 13:24:39 +0100 Subject: [PATCH 11/20] Do not update zstandard, update mamba --- stack/base/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stack/base/Dockerfile b/stack/base/Dockerfile index fb772ba7..05c936c0 100644 --- a/stack/base/Dockerfile +++ b/stack/base/Dockerfile @@ -48,7 +48,7 @@ COPY pip.conf /etc/pip.conf # Update async_generator, certipy to satisfy `pip check` # https://github.com/aiidalab/aiidalab-docker-stack/issues/490 # Install aiida-core and other shared requirements. -RUN mamba update -y pip zstandard async_generator certipy && \ +RUN mamba update -y pip mamba async_generator certipy && \ mamba install --yes \ aiida-core==${AIIDA_VERSION} \ mamba-bash-completion \ From ac9850c37f441d7408eb285de60a1c03e568407f Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sun, 8 Sep 2024 13:25:13 +0100 Subject: [PATCH 12/20] Revert full-stack fix-permission change --- stack/full-stack/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stack/full-stack/Dockerfile b/stack/full-stack/Dockerfile index cebeb532..61ea23a5 100644 --- a/stack/full-stack/Dockerfile +++ b/stack/full-stack/Dockerfile @@ -10,7 +10,7 @@ COPY --from=base "${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/${NB_USER}" +RUN fix-permissions "/home/${NB_USER}/.aiida" USER ${NB_USER} From 98d976c18ca199ad33a2f5d6755560384d417d4e Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sun, 8 Sep 2024 13:54:03 +0100 Subject: [PATCH 13/20] Update zstandard --- stack/base/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stack/base/Dockerfile b/stack/base/Dockerfile index 05c936c0..9033a5a3 100644 --- a/stack/base/Dockerfile +++ b/stack/base/Dockerfile @@ -48,7 +48,7 @@ COPY pip.conf /etc/pip.conf # Update async_generator, certipy to satisfy `pip check` # https://github.com/aiidalab/aiidalab-docker-stack/issues/490 # Install aiida-core and other shared requirements. -RUN mamba update -y pip mamba async_generator certipy && \ +RUN mamba update -y pip mamba zstandard async_generator certipy && \ mamba install --yes \ aiida-core==${AIIDA_VERSION} \ mamba-bash-completion \ From e830af4deb334cdd1526979532d67b52166b3755 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sun, 8 Sep 2024 15:06:51 +0100 Subject: [PATCH 14/20] Update comment --- stack/base/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/stack/base/Dockerfile b/stack/base/Dockerfile index 9033a5a3..0cd4c2d4 100644 --- a/stack/base/Dockerfile +++ b/stack/base/Dockerfile @@ -47,6 +47,7 @@ COPY pip.conf /etc/pip.conf # Upgrade pip and mamba to latest # Update async_generator, certipy to satisfy `pip check` # https://github.com/aiidalab/aiidalab-docker-stack/issues/490 +# Update zstandard, without this the `mamba install` command fails for unknown reason. # Install aiida-core and other shared requirements. RUN mamba update -y pip mamba zstandard async_generator certipy && \ mamba install --yes \ From 9f65faeb0421650fcea477e2b025ae0f0a6f72de Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sun, 8 Sep 2024 15:07:47 +0100 Subject: [PATCH 15/20] Try installing mamba==2.0.0rc4 --- stack/base/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/stack/base/Dockerfile b/stack/base/Dockerfile index 0cd4c2d4..91e9210f 100644 --- a/stack/base/Dockerfile +++ b/stack/base/Dockerfile @@ -53,6 +53,7 @@ RUN mamba update -y pip mamba zstandard async_generator certipy && \ mamba install --yes \ aiida-core==${AIIDA_VERSION} \ mamba-bash-completion \ + mamba==2.0.0rc4 \ && mamba clean --all -f -y && \ fix-permissions "${CONDA_DIR}" From f77b56a1c4895ce71be22946b6ba94975c7ce5b2 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sun, 8 Sep 2024 15:17:34 +0100 Subject: [PATCH 16/20] Revert "Try installing mamba==2.0.0rc4" This reverts commit 9f65faeb0421650fcea477e2b025ae0f0a6f72de. --- stack/base/Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/stack/base/Dockerfile b/stack/base/Dockerfile index 91e9210f..0cd4c2d4 100644 --- a/stack/base/Dockerfile +++ b/stack/base/Dockerfile @@ -53,7 +53,6 @@ RUN mamba update -y pip mamba zstandard async_generator certipy && \ mamba install --yes \ aiida-core==${AIIDA_VERSION} \ mamba-bash-completion \ - mamba==2.0.0rc4 \ && mamba clean --all -f -y && \ fix-permissions "${CONDA_DIR}" From cd167e5a036c1cfa41c6eeac22eba0bb6c898c25 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Thu, 24 Oct 2024 16:17:44 +0100 Subject: [PATCH 17/20] Pin mamba version to 1.5, 2.0 contains breaking changes --- stack/base/Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/stack/base/Dockerfile b/stack/base/Dockerfile index 5b820da1..289e923d 100644 --- a/stack/base/Dockerfile +++ b/stack/base/Dockerfile @@ -50,8 +50,9 @@ COPY pip.conf /etc/pip.conf # https://github.com/aiidalab/aiidalab-docker-stack/issues/490 # Update zstandard, without this the `mamba install` command fails for unknown reason. # Install aiida-core and other shared requirements. -RUN mamba update -y pip mamba zstandard async_generator certipy && \ +RUN mamba update -y pip zstandard async_generator certipy && \ mamba install --yes \ + mamba=1.5 \ aiida-core==${AIIDA_VERSION} \ mamba-bash-completion \ && mamba clean --all -f -y && \ From 674e96149bd7edcb6cd2f64909c8c7d7b67f4baf Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 2 Nov 2024 14:17:26 +0000 Subject: [PATCH 18/20] Run arm tests --- .github/workflows/main.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index fc3ee239..db627db5 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -58,9 +58,9 @@ jobs: # To save arm64 runner resources, we run the tests only on main # and only for full-stack image (same for integration tests below). test-arm64: - if: >- - github.repository == 'aiidalab/aiidalab-docker-stack' - && (github.ref_type == 'tag' || github.ref_name == 'main') + #if: >- + # github.repository == 'aiidalab/aiidalab-docker-stack' + # && (github.ref_type == 'tag' || github.ref_name == 'main') needs: build uses: ./.github/workflows/test.yml with: @@ -80,9 +80,9 @@ jobs: runner: [ubuntu-22.04, buildjet-4vcpu-ubuntu-2204-arm] isPR: - ${{ github.event_name == 'pull_request' }} - exclude: - - isPR: true - runner: buildjet-4vcpu-ubuntu-2204-arm + #exclude: + # - isPR: true + # runner: buildjet-4vcpu-ubuntu-2204-arm uses: ./.github/workflows/test.yml with: From aeaa70044bce2b4ff2b16fc6eabd5cb0901c5e0d Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Tue, 19 Nov 2024 19:02:12 +0100 Subject: [PATCH 19/20] to-be-reverted: Test aiidalab-home fix --- stack/lab/Dockerfile | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/stack/lab/Dockerfile b/stack/lab/Dockerfile index 0c2d29cd..a65e4415 100644 --- a/stack/lab/Dockerfile +++ b/stack/lab/Dockerfile @@ -30,9 +30,8 @@ RUN echo 'eval "$(_AIIDALAB_COMPLETE=bash_source aiidalab)"' >> "${CONDA_DIR}/et # Install the aiidalab-home app. ARG AIIDALAB_HOME_VERSION -RUN git clone https://github.com/aiidalab/aiidalab-home && \ +RUN git clone --branch fix/single_app_crash https://github.com/aiidalab/aiidalab-home && \ cd aiidalab-home && \ - git checkout v"${AIIDALAB_HOME_VERSION}" && \ pip install --no-user --quiet --no-cache-dir "./" && \ fix-permissions "./" && \ fix-permissions "${CONDA_DIR}" && \ From 4a4e2d7f466e8e654b030d06ac90e0433e377178 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Tue, 4 Feb 2025 14:09:05 +0000 Subject: [PATCH 20/20] Revert "to-be-reverted: Test aiidalab-home fix" This reverts commit aeaa70044bce2b4ff2b16fc6eabd5cb0901c5e0d. --- stack/lab/Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/stack/lab/Dockerfile b/stack/lab/Dockerfile index a65e4415..0c2d29cd 100644 --- a/stack/lab/Dockerfile +++ b/stack/lab/Dockerfile @@ -30,8 +30,9 @@ RUN echo 'eval "$(_AIIDALAB_COMPLETE=bash_source aiidalab)"' >> "${CONDA_DIR}/et # Install the aiidalab-home app. ARG AIIDALAB_HOME_VERSION -RUN git clone --branch fix/single_app_crash https://github.com/aiidalab/aiidalab-home && \ +RUN git clone https://github.com/aiidalab/aiidalab-home && \ cd aiidalab-home && \ + git checkout v"${AIIDALAB_HOME_VERSION}" && \ pip install --no-user --quiet --no-cache-dir "./" && \ fix-permissions "./" && \ fix-permissions "${CONDA_DIR}" && \