From 6278d85926d90866650612843ba04f12acd952c5 Mon Sep 17 00:00:00 2001 From: Devin Cowan Date: Tue, 3 Jun 2025 11:25:59 -0400 Subject: [PATCH 1/7] Remove specific version pinning for pyopenssl in Dockerfile to allow for automatic upgrades --- singleuser/csdms-tools/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/singleuser/csdms-tools/Dockerfile b/singleuser/csdms-tools/Dockerfile index 99da1c9..e327e57 100644 --- a/singleuser/csdms-tools/Dockerfile +++ b/singleuser/csdms-tools/Dockerfile @@ -8,7 +8,7 @@ ENV XDG_CACHE_HOME /home/$NB_USER/.cache/ # downgrade pyopenssl to 23.0.0 RUN mamba install -y \ --channel conda-forge \ -pyopenssl=23.0.0 \ +pyopenssl \ && mamba clean --all -f -y # pymt From 68a62e5f342ab464d745d249fadb1e98f1623d3a Mon Sep 17 00:00:00 2001 From: Devin Cowan Date: Tue, 3 Jun 2025 11:29:57 -0400 Subject: [PATCH 2/7] Remove specific version pinning for pymt_hydrotrend and pymt_sedflux in Dockerfile for flexibility --- singleuser/csdms-tools/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/singleuser/csdms-tools/Dockerfile b/singleuser/csdms-tools/Dockerfile index e327e57..45b7679 100644 --- a/singleuser/csdms-tools/Dockerfile +++ b/singleuser/csdms-tools/Dockerfile @@ -20,8 +20,8 @@ landlab==2.5.0 \ child==21.03.12 \ pymt_child==0.2.1 \ hydrotrend==3.1.4 \ -pymt_hydrotrend==0.2.2 \ -pymt_sedflux==0.2.0 \ +pymt_hydrotrend \ +pymt_sedflux \ sedflux==2.3.1 \ pymt_ecsimplesnow==0.2.6 \ pymt_gipl==0.1.1 \ From 9ed48e655bc2cd64c2b9d82ce0c35f70b190bc3d Mon Sep 17 00:00:00 2001 From: Devin Cowan Date: Tue, 3 Jun 2025 11:37:45 -0400 Subject: [PATCH 3/7] Update Dockerfile to clear conda pins and install dependencies from environment.yaml --- singleuser/csdms-tools/Dockerfile | 10 +++++++--- singleuser/csdms-tools/environment.yaml | 5 +++++ 2 files changed, 12 insertions(+), 3 deletions(-) create mode 100644 singleuser/csdms-tools/environment.yaml diff --git a/singleuser/csdms-tools/Dockerfile b/singleuser/csdms-tools/Dockerfile index 45b7679..2a42592 100644 --- a/singleuser/csdms-tools/Dockerfile +++ b/singleuser/csdms-tools/Dockerfile @@ -5,7 +5,11 @@ USER $NB_UID ENV XDG_CACHE_HOME /home/$NB_USER/.cache/ -# downgrade pyopenssl to 23.0.0 +RUN > /opt/conda/conda-meta/pinned # clear conda pins +COPY --chown=$NB_UID:$NB_UID environment.yaml /tmp/environment.yaml +RUN mamba env update -n base --file /tmp/environment.yaml \ + && mamba clean -afy + RUN mamba install -y \ --channel conda-forge \ pyopenssl \ @@ -20,8 +24,8 @@ landlab==2.5.0 \ child==21.03.12 \ pymt_child==0.2.1 \ hydrotrend==3.1.4 \ -pymt_hydrotrend \ -pymt_sedflux \ +pymt_hydrotrend==0.2.2 \ +pymt_sedflux==0.2.0 \ sedflux==2.3.1 \ pymt_ecsimplesnow==0.2.6 \ pymt_gipl==0.1.1 \ diff --git a/singleuser/csdms-tools/environment.yaml b/singleuser/csdms-tools/environment.yaml new file mode 100644 index 0000000..742fc04 --- /dev/null +++ b/singleuser/csdms-tools/environment.yaml @@ -0,0 +1,5 @@ +name: base +channels: + - conda-forge +dependencies: + - python==3.9.16 From ac82df144dece86d50194223212c05a71344b63d Mon Sep 17 00:00:00 2001 From: Devin Cowan Date: Tue, 3 Jun 2025 11:42:28 -0400 Subject: [PATCH 4/7] Set working directory to /opt in Dockerfile --- singleuser/csdms-tools/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/singleuser/csdms-tools/Dockerfile b/singleuser/csdms-tools/Dockerfile index 2a42592..761da2a 100644 --- a/singleuser/csdms-tools/Dockerfile +++ b/singleuser/csdms-tools/Dockerfile @@ -5,6 +5,7 @@ USER $NB_UID ENV XDG_CACHE_HOME /home/$NB_USER/.cache/ +WORKDIR /opt RUN > /opt/conda/conda-meta/pinned # clear conda pins COPY --chown=$NB_UID:$NB_UID environment.yaml /tmp/environment.yaml RUN mamba env update -n base --file /tmp/environment.yaml \ From 0d0e7678d04b5e5cc3f756e95a10e6f479eb48fd Mon Sep 17 00:00:00 2001 From: Devin Cowan Date: Tue, 3 Jun 2025 11:47:34 -0400 Subject: [PATCH 5/7] Remove pyopenssl upgrade to resolve nbfetch loading issue --- singleuser/csdms-tools/Dockerfile | 4 ---- 1 file changed, 4 deletions(-) diff --git a/singleuser/csdms-tools/Dockerfile b/singleuser/csdms-tools/Dockerfile index 761da2a..3d4227d 100644 --- a/singleuser/csdms-tools/Dockerfile +++ b/singleuser/csdms-tools/Dockerfile @@ -33,10 +33,6 @@ pymt_gipl==0.1.1 \ pymt_rafem==0.1.4 \ && mamba clean --all -f -y -# upgrade pyopenssl to fix an issue that is preventing -# nbfetch from loading correctly. -RUN mamba upgrade pyopenssl -y - # data component RUN mamba install -y \ From 37b319025134ce449f217c5d611235800316ea5a Mon Sep 17 00:00:00 2001 From: Devin Cowan Date: Tue, 3 Jun 2025 11:58:43 -0400 Subject: [PATCH 6/7] Set working directory to root after updating conda environment --- singleuser/csdms-tools/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/singleuser/csdms-tools/Dockerfile b/singleuser/csdms-tools/Dockerfile index 3d4227d..3558ac0 100644 --- a/singleuser/csdms-tools/Dockerfile +++ b/singleuser/csdms-tools/Dockerfile @@ -10,6 +10,7 @@ RUN > /opt/conda/conda-meta/pinned # clear conda pins COPY --chown=$NB_UID:$NB_UID environment.yaml /tmp/environment.yaml RUN mamba env update -n base --file /tmp/environment.yaml \ && mamba clean -afy +WORKDIR / RUN mamba install -y \ --channel conda-forge \ From c3e9c1cc8812442b75d96b32ef70e123691147f0 Mon Sep 17 00:00:00 2001 From: Devin Cowan Date: Tue, 3 Jun 2025 12:29:00 -0400 Subject: [PATCH 7/7] Add CONDA_PKG_DIRS environment variable to Dockerfile --- singleuser/csdms-tools/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/singleuser/csdms-tools/Dockerfile b/singleuser/csdms-tools/Dockerfile index 3558ac0..926bd3c 100644 --- a/singleuser/csdms-tools/Dockerfile +++ b/singleuser/csdms-tools/Dockerfile @@ -4,6 +4,7 @@ FROM cuahsi/singleuser-base:$BASE_VERSION USER $NB_UID ENV XDG_CACHE_HOME /home/$NB_USER/.cache/ +ENV CONDA_PKG_DIRS=$HOME/.conda/pkgs WORKDIR /opt RUN > /opt/conda/conda-meta/pinned # clear conda pins