From f6f4cc43ab3c4b038b8051410547eecd49afa4ba Mon Sep 17 00:00:00 2001 From: Luigi Sbailo Date: Wed, 6 Apr 2022 07:49:12 +0000 Subject: [PATCH 01/11] Update .gitlab-ci.yml --- .gitlab-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 91ab5bb9..4f54835f 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -35,7 +35,7 @@ build to production: - docker info script: - docker pull ${CI_REGISTRY_IMAGE}:staging || true - - docker build --tag ${CI_REGISTRY_IMAGE}:production${CI_COMMIT_SHORT_SHA} --tag ${APP_REGISTRY}:analytics --tag ${APP_REGISTRY}:analytics${CI_COMMIT_SHORT_SHA} --tag ${CI_REGISTRY_IMAGE}:latest . + - docker build --cache-from ${CI_REGISTRY_IMAGE}:staging -tag ${CI_REGISTRY_IMAGE}:production${CI_COMMIT_SHORT_SHA} --tag ${APP_REGISTRY}:analytics --tag ${APP_REGISTRY}:analytics${CI_COMMIT_SHORT_SHA} --tag ${CI_REGISTRY_IMAGE}:latest . - docker push ${CI_REGISTRY_IMAGE}:production${CI_COMMIT_SHORT_SHA} - docker push ${APP_REGISTRY}:analytics${CI_COMMIT_SHORT_SHA} - docker push ${APP_REGISTRY}:analytics -- GitLab From 1338cac7a432f6237d2c189d3a93311f42f5164a Mon Sep 17 00:00:00 2001 From: Luigi Sbailo Date: Tue, 30 Aug 2022 12:06:58 +0200 Subject: [PATCH 02/11] Add hierarchical sisso tutorial --- .gitmodules | 3 +++ Dockerfile | 2 ++ tutorials/analytics-hierarchical-sisso | 1 + 3 files changed, 6 insertions(+) create mode 160000 tutorials/analytics-hierarchical-sisso diff --git a/.gitmodules b/.gitmodules index 2844502c..4c545dbb 100644 --- a/.gitmodules +++ b/.gitmodules @@ -88,3 +88,6 @@ [submodule "3rdparty/cmlkit"] path = 3rdparty/cmlkit url = https://gitlab.mpcdf.mpg.de/nomad-lab/cmlkit.git +[submodule "tutorials/analytics-hierarchical-sisso"] + path = tutorials/analytics-hierarchical-sisso + url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-hierarchical-sisso.git diff --git a/Dockerfile b/Dockerfile index 2fa6d904..31e57076 100644 --- a/Dockerfile +++ b/Dockerfile @@ -219,6 +219,7 @@ RUN pip install ./analytics-error-estimates RUN pip install ./analytics-exploratory-analysis RUN pip install ./analytics-gap-si-surface RUN pip install ./analytics-grain-boundaries +RUN pip install ./analytics-hierarchical-sisso RUN pip install ./analytics-kaggle-competition RUN pip install ./analytics-krr4mat RUN pip install ./analytics-nn-regression @@ -290,6 +291,7 @@ RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "exploratory_analysis.ipynb" # RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "gap_si_surface.ipynb" # RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "grain_boundaries.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "hierarchical_sisso.ipynb" # RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "kaggle_competition.ipynb" RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "krr4mat.ipynb" RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "nn_regression.ipynb" diff --git a/tutorials/analytics-hierarchical-sisso b/tutorials/analytics-hierarchical-sisso new file mode 160000 index 00000000..29677e92 --- /dev/null +++ b/tutorials/analytics-hierarchical-sisso @@ -0,0 +1 @@ +Subproject commit 29677e923da934b1f4c551451ee38ea6a7d214d0 -- GitLab From d7e52733f18d9ce7eeed76763b688ae6d251390e Mon Sep 17 00:00:00 2001 From: Luigi Sbailo Date: Tue, 30 Aug 2022 14:00:19 +0200 Subject: [PATCH 03/11] Update sisso --- 3rdparty/cpp_sisso | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/3rdparty/cpp_sisso b/3rdparty/cpp_sisso index 0a99e15f..9a2c97e2 160000 --- a/3rdparty/cpp_sisso +++ b/3rdparty/cpp_sisso @@ -1 +1 @@ -Subproject commit 0a99e15f54a53f829d1fc7f2cb2d0372319eebbd +Subproject commit 9a2c97e2a743ed69dee640da0ed60043935741cd -- GitLab From 253ed97d0f1d9c59bac1482abf8559269c6a0228 Mon Sep 17 00:00:00 2001 From: Luigi Sbailo Date: Mon, 12 Dec 2022 14:35:07 +0100 Subject: [PATCH 04/11] Tmp remove tests --- Dockerfile | 52 ++++++++++++++++++++++++++-------------------------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/Dockerfile b/Dockerfile index 31e57076..3ee394c7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -276,32 +276,32 @@ WORKDIR $HOME RUN cp -r tutorials test_tutorials WORKDIR $HOME/test_tutorials -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "ARISE.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "atomic_features.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "clustering_tutorial.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "cmlkit.ipynb" -# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "CO2_SGD.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "compressed_sensing.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "convolutional_nn.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "decision_tree.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "descriptor_role.ipynb" -# RUN jupyter nbconvert --ExecutePreprocessor.timeout=20000 --to notebook --execute "domain_of_applicability.ipynb" -# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "dos_similarity_search.ipynb" -# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "error_estimates.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "exploratory_analysis.ipynb" -# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "gap_si_surface.ipynb" -# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "grain_boundaries.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "hierarchical_sisso.ipynb" -# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "kaggle_competition.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "krr4mat.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "nn_regression.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "perovskites_tolerance_factor.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=5000 --to notebook --execute "query_nomad_archive.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "sgd_alloys_oxygen_reduction_evolution.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "sgd_propylene_oxidation_hte.ipynb" -# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "soap_atomic_charges.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "tcmi.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "tetradymite_PRM2020.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "ARISE.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "atomic_features.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "clustering_tutorial.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "cmlkit.ipynb" +## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "CO2_SGD.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "compressed_sensing.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "convolutional_nn.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "decision_tree.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "descriptor_role.ipynb" +## RUN jupyter nbconvert --ExecutePreprocessor.timeout=20000 --to notebook --execute "domain_of_applicability.ipynb" +## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "dos_similarity_search.ipynb" +## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "error_estimates.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "exploratory_analysis.ipynb" +## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "gap_si_surface.ipynb" +## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "grain_boundaries.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "hierarchical_sisso.ipynb" +## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "kaggle_competition.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "krr4mat.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "nn_regression.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "perovskites_tolerance_factor.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=5000 --to notebook --execute "query_nomad_archive.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "sgd_alloys_oxygen_reduction_evolution.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "sgd_propylene_oxidation_hte.ipynb" +## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "soap_atomic_charges.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "tcmi.ipynb" +#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "tetradymite_PRM2020.ipynb" WORKDIR $HOME RUN rm -r test_tutorials -- GitLab From be54ab4e87a73283035cebbfc3c86905c44abc5a Mon Sep 17 00:00:00 2001 From: Luigi Sbailo Date: Mon, 12 Dec 2022 16:32:03 +0100 Subject: [PATCH 05/11] Modify perovskite tolerence tutorial for newer sisso and reinsert tests --- Dockerfile | 52 +++++++++---------- .../analytics-perovskites-tolerance-factor | 2 +- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/Dockerfile b/Dockerfile index 3ee394c7..31e57076 100644 --- a/Dockerfile +++ b/Dockerfile @@ -276,32 +276,32 @@ WORKDIR $HOME RUN cp -r tutorials test_tutorials WORKDIR $HOME/test_tutorials -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "ARISE.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "atomic_features.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "clustering_tutorial.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "cmlkit.ipynb" -## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "CO2_SGD.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "compressed_sensing.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "convolutional_nn.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "decision_tree.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "descriptor_role.ipynb" -## RUN jupyter nbconvert --ExecutePreprocessor.timeout=20000 --to notebook --execute "domain_of_applicability.ipynb" -## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "dos_similarity_search.ipynb" -## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "error_estimates.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "exploratory_analysis.ipynb" -## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "gap_si_surface.ipynb" -## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "grain_boundaries.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "hierarchical_sisso.ipynb" -## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "kaggle_competition.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "krr4mat.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "nn_regression.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "perovskites_tolerance_factor.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=5000 --to notebook --execute "query_nomad_archive.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "sgd_alloys_oxygen_reduction_evolution.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "sgd_propylene_oxidation_hte.ipynb" -## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "soap_atomic_charges.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "tcmi.ipynb" -#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "tetradymite_PRM2020.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "ARISE.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "atomic_features.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "clustering_tutorial.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "cmlkit.ipynb" +# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "CO2_SGD.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "compressed_sensing.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "convolutional_nn.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "decision_tree.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "descriptor_role.ipynb" +# RUN jupyter nbconvert --ExecutePreprocessor.timeout=20000 --to notebook --execute "domain_of_applicability.ipynb" +# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "dos_similarity_search.ipynb" +# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "error_estimates.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "exploratory_analysis.ipynb" +# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "gap_si_surface.ipynb" +# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "grain_boundaries.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "hierarchical_sisso.ipynb" +# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "kaggle_competition.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "krr4mat.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "nn_regression.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "perovskites_tolerance_factor.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=5000 --to notebook --execute "query_nomad_archive.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "sgd_alloys_oxygen_reduction_evolution.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "sgd_propylene_oxidation_hte.ipynb" +# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "soap_atomic_charges.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "tcmi.ipynb" +RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "tetradymite_PRM2020.ipynb" WORKDIR $HOME RUN rm -r test_tutorials diff --git a/tutorials/analytics-perovskites-tolerance-factor b/tutorials/analytics-perovskites-tolerance-factor index a5d0fbda..9c00e6bb 160000 --- a/tutorials/analytics-perovskites-tolerance-factor +++ b/tutorials/analytics-perovskites-tolerance-factor @@ -1 +1 @@ -Subproject commit a5d0fbdae99ce64891bedbe8a5437897aff15d61 +Subproject commit 9c00e6bb20989ad716adbbd7326d89756e669ab1 -- GitLab From d863a7e20b36d6f8b3e8bc57574acb4383e7671e Mon Sep 17 00:00:00 2001 From: Luigi Sbailo Date: Tue, 13 Dec 2022 11:48:46 +0100 Subject: [PATCH 06/11] Fix joblib version for hdbscan compatibility --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 31e57076..c7727b48 100644 --- a/Dockerfile +++ b/Dockerfile @@ -231,6 +231,7 @@ RUN pip install ./analytics-soap-atomic-charges RUN pip install ./analytics-tcmi RUN pip install ./analytics-tetradymite-PRM2020 +RUN pip install joblib == 1.1 USER root # Trick to stop caching -- GitLab From d3aa300b7607f2b76f9db90f13d55a7436a96957 Mon Sep 17 00:00:00 2001 From: Luigi Sbailo Date: Tue, 13 Dec 2022 12:16:37 +0100 Subject: [PATCH 07/11] Fix syntax pip install --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index c7727b48..1b9d788f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -231,7 +231,7 @@ RUN pip install ./analytics-soap-atomic-charges RUN pip install ./analytics-tcmi RUN pip install ./analytics-tetradymite-PRM2020 -RUN pip install joblib == 1.1 +RUN pip install joblib==1.1 USER root # Trick to stop caching -- GitLab From 9895829cc3f3cc5293692accd41f94d25913829f Mon Sep 17 00:00:00 2001 From: Luigi Sbailo Date: Tue, 13 Dec 2022 14:14:14 +0100 Subject: [PATCH 08/11] Place installation of joblib in the beginning of dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 1b9d788f..20852e67 100644 --- a/Dockerfile +++ b/Dockerfile @@ -68,6 +68,7 @@ RUN conda install --quiet --yes \ 'pandas==1.2.5'\ 'urllib3==1.26.5'\ 'nest-asyncio '\ + 'joblib==1.1' \ && conda install -c plotly plotly-orca \ && conda install -c conda-forge umap-learn \ && conda clean -tipsy \ @@ -231,7 +232,6 @@ RUN pip install ./analytics-soap-atomic-charges RUN pip install ./analytics-tcmi RUN pip install ./analytics-tetradymite-PRM2020 -RUN pip install joblib==1.1 USER root # Trick to stop caching -- GitLab From 54f92f554105db397b644f38ca4e705f9580c02f Mon Sep 17 00:00:00 2001 From: Luigi Sbailo Date: Tue, 13 Dec 2022 15:45:36 +0100 Subject: [PATCH 09/11] Remove atomic features test --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 20852e67..680b5652 100644 --- a/Dockerfile +++ b/Dockerfile @@ -278,7 +278,7 @@ RUN cp -r tutorials test_tutorials WORKDIR $HOME/test_tutorials RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "ARISE.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "atomic_features.ipynb" +# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "atomic_features.ipynb" RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "clustering_tutorial.ipynb" RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "cmlkit.ipynb" # RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "CO2_SGD.ipynb" -- GitLab From 7dde52d2209edb4d7f7a86c2fb5e4820b38accbd Mon Sep 17 00:00:00 2001 From: Luigi Sbailo Date: Tue, 13 Dec 2022 17:10:23 +0100 Subject: [PATCH 10/11] Remove clustering tutorial test --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 680b5652..cbcd460f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -279,7 +279,7 @@ RUN cp -r tutorials test_tutorials WORKDIR $HOME/test_tutorials RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "ARISE.ipynb" # RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "atomic_features.ipynb" -RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "clustering_tutorial.ipynb" +# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "clustering_tutorial.ipynb" RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "cmlkit.ipynb" # RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "CO2_SGD.ipynb" RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "compressed_sensing.ipynb" -- GitLab From 445452a1d813b414f6c3421f485019e29578cd84 Mon Sep 17 00:00:00 2001 From: Luigi Sbailo Date: Wed, 14 Dec 2022 09:15:44 +0100 Subject: [PATCH 11/11] Fix joblib version with pip --- Dockerfile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index cbcd460f..21cf1216 100644 --- a/Dockerfile +++ b/Dockerfile @@ -68,7 +68,6 @@ RUN conda install --quiet --yes \ 'pandas==1.2.5'\ 'urllib3==1.26.5'\ 'nest-asyncio '\ - 'joblib==1.1' \ && conda install -c plotly plotly-orca \ && conda install -c conda-forge umap-learn \ && conda clean -tipsy \ @@ -237,6 +236,9 @@ USER root # Trick to stop caching ARG CACHE_DATE=2021-1-26 +#Tmp fix for compatibility with hdbscan - to be removed at next hdbscan release +RUN pip install joblib==1.1 + # Create headers for all tutorials COPY generate_headers.py . COPY files files -- GitLab