From 1e772b28ae372d9e8551105d1b61cf8ef8825493 Mon Sep 17 00:00:00 2001 From: Jason Boutte Date: Mon, 29 Jan 2024 12:54:44 -0800 Subject: [PATCH 01/10] Test change to postBuild --- .binder/postBuild | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.binder/postBuild b/.binder/postBuild index 3fbfa971b..9183ef651 100755 --- a/.binder/postBuild +++ b/.binder/postBuild @@ -1,3 +1,2 @@ #!/bin/bash -set -eux -python -m pip install -vv --no-deps --no-build-isolation -e . +python -m pip install -vv --no-deps --no-build-isolation . From 348038eedd1a0ac97a67477064dd31213d30b661 Mon Sep 17 00:00:00 2001 From: Jason Boutte Date: Mon, 29 Jan 2024 14:50:42 -0800 Subject: [PATCH 02/10] Removes binderhub customization --- .binder/postBuild | 2 -- apt.txt | 11 ----------- 2 files changed, 13 deletions(-) delete mode 100755 .binder/postBuild delete mode 100644 apt.txt diff --git a/.binder/postBuild b/.binder/postBuild deleted file mode 100755 index 9183ef651..000000000 --- a/.binder/postBuild +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -python -m pip install -vv --no-deps --no-build-isolation . diff --git a/apt.txt b/apt.txt deleted file mode 100644 index 58b2b22a3..000000000 --- a/apt.txt +++ /dev/null @@ -1,11 +0,0 @@ -dvipng -ghostscript -texlive-fonts-recommended -texlive-generic-recommended -texlive-latex-base -texlive-latex-extra -texlive-latex-recommended -texlive-publishers -texlive-science -texlive-xetex -cm-super From e9cdb6564fd8a6c6c3eca73db3581fdb7f3aa2d0 Mon Sep 17 00:00:00 2001 From: Jason Boutte Date: Mon, 29 Jan 2024 15:17:50 -0800 Subject: [PATCH 03/10] Adds postbuild script --- .binder/postBuild | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 .binder/postBuild diff --git a/.binder/postBuild b/.binder/postBuild new file mode 100644 index 000000000..0f4c367c3 --- /dev/null +++ b/.binder/postBuild @@ -0,0 +1,3 @@ +#!/bin/bash + +pip install -e . From ed9d417833dc9993482167a36538d0f00c7ceaa1 Mon Sep 17 00:00:00 2001 From: Jason Boutte Date: Mon, 29 Jan 2024 15:45:07 -0800 Subject: [PATCH 04/10] Replaces postBuild with separate environment.yml --- .binder/environment.yml | 58 +++++++++++++++++++++++++++++++++++++++++ .binder/postBuild | 3 --- 2 files changed, 58 insertions(+), 3 deletions(-) create mode 100644 .binder/environment.yml delete mode 100644 .binder/postBuild diff --git a/.binder/environment.yml b/.binder/environment.yml new file mode 100644 index 000000000..22ba21afe --- /dev/null +++ b/.binder/environment.yml @@ -0,0 +1,58 @@ +# Conda pcmdi_metrics development environment +name: pcmdi_metrics_dev +channels: + - conda-forge + - defaults +dependencies: + # ================== + # Base + # ================== + # NOTE: If versions are updated, also `additional_dependencies` list for mypy in `.pre-commit-config.yaml` + - python=3.10.10 + - pip=23.1.2 + - numpy=1.23.5 + - cartopy=0.22.0 + - matplotlib=3.7.1 + - cdat_info=8.2.1 + - cdms2=3.1.5 + - genutil=8.2.1 + - cdutil=8.2.1 + - cdp=1.7.0 + - eofs=1.4.0 + - seaborn=0.12.2 + - enso_metrics=1.1.1 + - xcdat>=0.6.1 + - xmltodict=0.13.0 + - setuptools=67.7.2 + - netcdf4=1.6.3 + - regionmask=0.9.0 + - rasterio=1.3.6 + - shapely=2.0.1 + - numdifftools + - nc-time-axis + # ================== + # Testing + # ================== + - pre_commit=3.2.2 + - pytest=7.3.1 + - pytest-cov=4.0.0 + # ================== + # Developer Tools + # ================== + - jupyterlab=3.6.3 + - nb_conda=2.2.1 + - nb_conda_kernels=2.3.1 + # ================== + # Documentation + # ================== + - sphinx=5.3.0 + - sphinx-autosummary-accessors=2022.4.0 + - sphinx-book-theme=1.0.1 + - sphinx-copybutton=0.5.1 + - nbsphinx=0.9.1 + - pandoc=3.1.1 + - ipython=8.11.0 # Required for nbsphinx syntax highlighting + - pip: + - pcmdi_metrics + +prefix: /opt/miniconda3/envs/pmcdi_metrics_dev diff --git a/.binder/postBuild b/.binder/postBuild deleted file mode 100644 index 0f4c367c3..000000000 --- a/.binder/postBuild +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -pip install -e . From 9ee79d1b20b652db536f2210756ec45cf4525929 Mon Sep 17 00:00:00 2001 From: Jason Boutte Date: Mon, 29 Jan 2024 15:53:44 -0800 Subject: [PATCH 05/10] Adds postBuild back --- .binder/environment.yml | 2 -- .binder/postBuild | 3 +++ 2 files changed, 3 insertions(+), 2 deletions(-) create mode 100644 .binder/postBuild diff --git a/.binder/environment.yml b/.binder/environment.yml index 22ba21afe..539bac09e 100644 --- a/.binder/environment.yml +++ b/.binder/environment.yml @@ -52,7 +52,5 @@ dependencies: - nbsphinx=0.9.1 - pandoc=3.1.1 - ipython=8.11.0 # Required for nbsphinx syntax highlighting - - pip: - - pcmdi_metrics prefix: /opt/miniconda3/envs/pmcdi_metrics_dev diff --git a/.binder/postBuild b/.binder/postBuild new file mode 100644 index 000000000..0f4c367c3 --- /dev/null +++ b/.binder/postBuild @@ -0,0 +1,3 @@ +#!/bin/bash + +pip install -e . From b181df592d98072710b3b5ebad1a0e2d3451b66e Mon Sep 17 00:00:00 2001 From: Jason Boutte Date: Tue, 30 Jan 2024 10:10:03 -0800 Subject: [PATCH 06/10] Adds packages --- .binder/apt.txt | 1 + 1 file changed, 1 insertion(+) create mode 100644 .binder/apt.txt diff --git a/.binder/apt.txt b/.binder/apt.txt new file mode 100644 index 000000000..b23368faa --- /dev/null +++ b/.binder/apt.txt @@ -0,0 +1 @@ +texlive-xetex From 70b759b7ca4db328e6679fa15d1b4f983dcd8667 Mon Sep 17 00:00:00 2001 From: Jason Boutte Date: Tue, 30 Jan 2024 10:26:17 -0800 Subject: [PATCH 07/10] Adds more texlive dependencies --- .binder/apt.txt | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.binder/apt.txt b/.binder/apt.txt index b23368faa..c1da1e228 100644 --- a/.binder/apt.txt +++ b/.binder/apt.txt @@ -1 +1,6 @@ +texlive-science texlive-xetex +texlive-font-utils +texlive-fonts-extra +texlive-fonts-recommended +texlive-latex-recommended From 7808e4def8baa4bd0002864dd26ad1ee50d29225 Mon Sep 17 00:00:00 2001 From: Jason Boutte Date: Tue, 30 Jan 2024 10:51:40 -0800 Subject: [PATCH 08/10] Adds meta package --- .binder/apt.txt | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/.binder/apt.txt b/.binder/apt.txt index c1da1e228..0d0331bf8 100644 --- a/.binder/apt.txt +++ b/.binder/apt.txt @@ -1,6 +1 @@ -texlive-science -texlive-xetex -texlive-font-utils -texlive-fonts-extra -texlive-fonts-recommended -texlive-latex-recommended +texlive-full From 55fdb8b8e9722eeeb4a5710a76435bec4114822a Mon Sep 17 00:00:00 2001 From: Jason Boutte Date: Wed, 31 Jan 2024 08:57:45 -0800 Subject: [PATCH 09/10] Removes editable mode, to install shared resources correctly --- .binder/postBuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.binder/postBuild b/.binder/postBuild index 0f4c367c3..c8a24fc87 100644 --- a/.binder/postBuild +++ b/.binder/postBuild @@ -1,3 +1,3 @@ #!/bin/bash -pip install -e . +pip install . From 331ad0bdd210570a29b26d72f894534e38e75e45 Mon Sep 17 00:00:00 2001 From: Jason Boutte Date: Thu, 1 Feb 2024 16:52:10 -0800 Subject: [PATCH 10/10] Remove top-level environment and symlink environment under .binder --- .binder/environment.yml | 57 +---------------------------------------- environment.yml | 1 - 2 files changed, 1 insertion(+), 57 deletions(-) mode change 100644 => 120000 .binder/environment.yml delete mode 120000 environment.yml diff --git a/.binder/environment.yml b/.binder/environment.yml deleted file mode 100644 index 539bac09e..000000000 --- a/.binder/environment.yml +++ /dev/null @@ -1,56 +0,0 @@ -# Conda pcmdi_metrics development environment -name: pcmdi_metrics_dev -channels: - - conda-forge - - defaults -dependencies: - # ================== - # Base - # ================== - # NOTE: If versions are updated, also `additional_dependencies` list for mypy in `.pre-commit-config.yaml` - - python=3.10.10 - - pip=23.1.2 - - numpy=1.23.5 - - cartopy=0.22.0 - - matplotlib=3.7.1 - - cdat_info=8.2.1 - - cdms2=3.1.5 - - genutil=8.2.1 - - cdutil=8.2.1 - - cdp=1.7.0 - - eofs=1.4.0 - - seaborn=0.12.2 - - enso_metrics=1.1.1 - - xcdat>=0.6.1 - - xmltodict=0.13.0 - - setuptools=67.7.2 - - netcdf4=1.6.3 - - regionmask=0.9.0 - - rasterio=1.3.6 - - shapely=2.0.1 - - numdifftools - - nc-time-axis - # ================== - # Testing - # ================== - - pre_commit=3.2.2 - - pytest=7.3.1 - - pytest-cov=4.0.0 - # ================== - # Developer Tools - # ================== - - jupyterlab=3.6.3 - - nb_conda=2.2.1 - - nb_conda_kernels=2.3.1 - # ================== - # Documentation - # ================== - - sphinx=5.3.0 - - sphinx-autosummary-accessors=2022.4.0 - - sphinx-book-theme=1.0.1 - - sphinx-copybutton=0.5.1 - - nbsphinx=0.9.1 - - pandoc=3.1.1 - - ipython=8.11.0 # Required for nbsphinx syntax highlighting - -prefix: /opt/miniconda3/envs/pmcdi_metrics_dev diff --git a/.binder/environment.yml b/.binder/environment.yml new file mode 120000 index 000000000..3a53b8dc8 --- /dev/null +++ b/.binder/environment.yml @@ -0,0 +1 @@ +../conda-env/dev.yml \ No newline at end of file diff --git a/environment.yml b/environment.yml deleted file mode 120000 index 05c4383d4..000000000 --- a/environment.yml +++ /dev/null @@ -1 +0,0 @@ -./conda-env/dev.yml \ No newline at end of file