Merge pull request #5 from esgf-nimbus/update-minimal-notebook

Update minimal notebook

.gitignore

@@ -0,0 +1,2 @@
+changelog.md
+**/.ipynb_checkpoints

dockerfiles/Makefile

@@ -4,11 +4,14 @@ NAMESPACE ?= ghcr.io/esgf-nimbus
 
 build push run: REPOSITORY = $(lastword $(subst /, ,$(PWD)))
 
-build:
+build: changelog
 	docker build $(ARGS) -t $(NAMESPACE)/$(REPOSITORY):$(VERSION) .
 
 push:
 	docker push $(NAMESPACE)/$(REPOSITORY):$(VERSION)
 
 run:
 	docker run -it $(ARGS) $(if $(ENTRYPOINT),--entrypoint $(ENTRYPOINT),) $(NAMESPACE)/$(REPOSITORY):$(VERSION) $(COMMAND)
+
+changelog:
+	git log --pretty="%s" . | python -c "import sys;lines=[f'- {x}' if 'Bump' in x else f'  - {x}' for x in sys.stdin]; print(''.join(['# Changelog\n'] + lines))" > changelog.md

dockerfiles/dask-gateway/Makefile

@@ -5,7 +5,7 @@ VERSION = 0.1.0
 .PHONY: env-export
 env-export: ARGS = -v $(PWD)/../minimal-notebook/conda-envs:/conda-envs
 env-export: ENTRYPOINT = /bin/bash
-env-export: COMMAND = -c "conda env export -n dask-gateway -f /conda-envs/dask-gateway.yaml"
+env-export: COMMAND = -c "conda env export -f /conda-envs/dask-gateway.yaml"
 env-export: run
 
 include ../Makefile

dockerfiles/minimal-notebook-gpu/Dockerfile

@@ -9,4 +9,8 @@ RUN --mount=type=cache,target=/opt/conda/pkgs \
 	cupy && \
 	chown -R ${NB_UID}:${NB_GID} /home/jovyan
 
+COPY changelog.md /changelog.md
+
+RUN source /scripts/render-intro.sh
+
 USER $NB_USER

dockerfiles/minimal-notebook-gpu/Makefile

@@ -1,7 +1,9 @@
 .DEFAULT_GOAL = build
 
-VERSION = 0.1.0
+VERSION = 0.1.1
 
 build: ARGS = --build-arg TAG=$(shell tbump -C ../minimal-notebook current-version)
 
+run: ARGS = -p 8888:8888
+
 include ../Makefile

dockerfiles/minimal-notebook-gpu/tbump.toml

@@ -1,5 +1,5 @@
 [version]
-current = "0.1.0"
+current = "0.1.1"
 
 regex = '''
   (?P<major>\d+)

dockerfiles/minimal-notebook/Dockerfile

@@ -28,14 +28,28 @@ RUN groupadd -g 1026 climate && \
     pip install nbgitpuller && \
     mkdir /notebooks
 
-COPY notebooks /notebooks
 COPY conda-envs /conda-envs
 
 RUN --mount=type=cache,target=/opt/conda/pkgs \
-    mamba env create -n dask-gateway -f /conda-envs/dask-gateway.yaml && \
-    source /opt/conda/etc/profile.d/conda.sh && \
-    conda activate dask-gateway && \
-    python -m ipykernel install --name=dask-gateway && \
+    mamba install -y \
+        xcdat \
+        xarray \
+        netcdf4 \
+        intake \
+        intake-esm \
+        intake-stac \
+        intake-xarray \
+        intake-dataframe-catalog
+
+COPY scripts /scripts
+
+RUN --mount=type=cache,target=/opt/conda/pkgs \
+    source /scripts/install-envs.sh && \
     chown -R ${NB_UID}:${NB_GID} /home/jovyan
 
+COPY notebooks /notebooks
+COPY changelog.md /changelog.md
+
+RUN source /scripts/render-intro.sh
+
 USER $NB_USER

dockerfiles/minimal-notebook/Makefile

@@ -1,6 +1,6 @@
 .DEFAULT_GOAL = build
 
-VERSION = 0.1.7
+VERSION = 0.1.8
 
 run: ARGS = -p 8888:8888
 

dockerfiles/minimal-notebook/conda-envs/dask-gateway.yaml

@@ -1,4 +1,211 @@
-name: dask-gateway
+name: base
 channels:
   - conda-forge
-prefix: /opt/conda/envs/dask-gateway
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - aiohttp=3.8.5=py310h2372a71_0
+  - aiosignal=1.3.1=pyhd8ed1ab_0
+  - asttokens=2.2.1=pyhd8ed1ab_0
+  - async-timeout=4.0.2=pyhd8ed1ab_0
+  - attrs=23.1.0=pyh71513ae_1
+  - aws-c-auth=0.7.0=hf8751d9_2
+  - aws-c-cal=0.6.0=h93469e0_0
+  - aws-c-common=0.8.23=hd590300_0
+  - aws-c-compression=0.2.17=h862ab75_1
+  - aws-c-event-stream=0.3.1=h9599702_1
+  - aws-c-http=0.7.11=hbe98c3e_0
+  - aws-c-io=0.13.28=h3870b5a_0
+  - aws-c-mqtt=0.8.14=h2e270ba_2
+  - aws-c-s3=0.3.13=heb0bb06_2
+  - aws-c-sdkutils=0.1.11=h862ab75_1
+  - aws-checksums=0.1.16=h862ab75_1
+  - aws-crt-cpp=0.20.3=he9c0e7f_4
+  - aws-sdk-cpp=1.10.57=hbc2ea52_17
+  - backcall=0.2.0=pyh9f0ad1d_0
+  - backports=1.0=pyhd8ed1ab_3
+  - backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0
+  - blosc=1.21.4=h0f2a231_0
+  - bokeh=2.4.3=pyhd8ed1ab_3
+  - brotli-python=1.0.9=py310hd8f1fbe_9
+  - bzip2=1.0.8=h7f98852_4
+  - c-ares=1.19.1=hd590300_0
+  - ca-certificates=2023.5.7=hbcca054_0
+  - certifi=2023.5.7=pyhd8ed1ab_0
+  - cffi=1.15.1=py310h255011f_3
+  - cftime=1.6.2=py310hde88566_1
+  - charset-normalizer=3.2.0=pyhd8ed1ab_0
+  - click=8.1.6=unix_pyh707e725_0
+  - cloudpickle=2.2.1=pyhd8ed1ab_0
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - comm=0.1.3=pyhd8ed1ab_0
+  - conda=23.1.0=py310hff52083_0
+  - conda-package-handling=2.0.2=pyh38be061_0
+  - conda-package-streaming=0.8.0=pyhd8ed1ab_0
+  - cryptography=41.0.2=py310h75e40e8_0
+  - cytoolz=0.12.2=py310h2372a71_0
+  - dask=2023.7.1=pyhd8ed1ab_0
+  - dask-core=2023.7.1=pyhd8ed1ab_0
+  - dask-gateway=2023.1.1=pyh8af1aa0_0
+  - debugpy=1.6.7=py310heca2aa9_0
+  - decorator=5.1.1=pyhd8ed1ab_0
+  - distributed=2023.7.1=pyhd8ed1ab_0
+  - executing=1.2.0=pyhd8ed1ab_0
+  - fmt=9.1.0=h924138e_0
+  - freetype=2.12.1=hca18f0e_1
+  - frozenlist=1.4.0=py310h2372a71_0
+  - fsspec=2023.6.0=pyh1a96a4e_0
+  - gflags=2.2.2=he1b5a44_1004
+  - glog=0.6.0=h6f12383_0
+  - hdf4=4.2.15=h501b40f_6
+  - hdf5=1.14.1=nompi_h4f84152_100
+  - icu=72.1=hcb278e6_0
+  - idna=3.4=pyhd8ed1ab_0
+  - importlib-metadata=6.8.0=pyha770c72_0
+  - importlib_metadata=6.8.0=hd8ed1ab_0
+  - ipykernel=6.24.0=pyh71e2992_0
+  - ipython=8.14.0=pyh41d4057_0
+  - jedi=0.18.2=pyhd8ed1ab_0
+  - jinja2=3.1.2=pyhd8ed1ab_1
+  - jupyter_client=8.3.0=pyhd8ed1ab_0
+  - jupyter_core=5.3.1=py310hff52083_0
+  - keyutils=1.6.1=h166bdaf_0
+  - krb5=1.21.1=h659d440_0
+  - lcms2=2.15=haa2dc70_1
+  - ld_impl_linux-64=2.40=h41732ed_0
+  - lerc=4.0.0=h27087fc_0
+  - libabseil=20230125.3=cxx17_h59595ed_0
+  - libaec=1.0.6=hcb278e6_1
+  - libarchive=3.6.2=h039dbb9_1
+  - libarrow=12.0.1=h657c46f_5_cpu
+  - libblas=3.9.0=17_linux64_openblas
+  - libbrotlicommon=1.0.9=h166bdaf_9
+  - libbrotlidec=1.0.9=h166bdaf_9
+  - libbrotlienc=1.0.9=h166bdaf_9
+  - libcblas=3.9.0=17_linux64_openblas
+  - libcrc32c=1.1.2=h9c3ff4c_0
+  - libcurl=8.1.2=hca28451_1
+  - libdeflate=1.18=h0b41bf4_0
+  - libedit=3.1.20191231=he28a2e2_2
+  - libev=4.33=h516909a_1
+  - libevent=2.1.12=hf998b51_1
+  - libffi=3.4.2=h7f98852_5
+  - libgcc-ng=13.1.0=he5830b7_0
+  - libgfortran-ng=13.1.0=h69a702a_0
+  - libgfortran5=13.1.0=h15d22d2_0
+  - libgomp=13.1.0=he5830b7_0
+  - libgoogle-cloud=2.12.0=h840a212_1
+  - libgrpc=1.56.2=h3905398_0
+  - libiconv=1.17=h166bdaf_0
+  - libjpeg-turbo=2.1.5.1=h0b41bf4_0
+  - liblapack=3.9.0=17_linux64_openblas
+  - libmamba=1.4.2=hcea66bb_0
+  - libmambapy=1.4.2=py310h1428755_0
+  - libnetcdf=4.9.2=nompi_h7e745eb_109
+  - libnghttp2=1.52.0=h61bc06f_0
+  - libnsl=2.0.0=h7f98852_0
+  - libnuma=2.0.16=h0b41bf4_1
+  - libopenblas=0.3.23=pthreads_h80387f5_0
+  - libpng=1.6.39=h753d276_0
+  - libprotobuf=4.23.3=hd1fb520_0
+  - libsodium=1.0.18=h36c2ea0_1
+  - libsolv=0.7.24=hfc55251_1
+  - libsqlite=3.42.0=h2797004_0
+  - libssh2=1.11.0=h0841786_0
+  - libstdcxx-ng=13.1.0=hfd8a6a1_0
+  - libthrift=0.18.1=h8fd135c_2
+  - libtiff=4.5.1=h8b53f26_0
+  - libutf8proc=2.8.0=h166bdaf_0
+  - libuuid=2.38.1=h0b41bf4_0
+  - libwebp-base=1.3.1=hd590300_0
+  - libxcb=1.15=h0b41bf4_0
+  - libxml2=2.11.4=h0d562d8_0
+  - libzip=1.9.2=hc929e4a_1
+  - libzlib=1.2.13=hd590300_5
+  - locket=1.0.0=pyhd8ed1ab_0
+  - lz4=4.3.2=py310h0cfdcf0_0
+  - lz4-c=1.9.4=hcb278e6_0
+  - lzo=2.10=h516909a_1000
+  - mamba=1.4.2=py310h51d5547_0
+  - markupsafe=2.1.3=py310h2372a71_0
+  - matplotlib-inline=0.1.6=pyhd8ed1ab_0
+  - msgpack-python=1.0.5=py310hdf3cbec_0
+  - multidict=6.0.4=py310h1fa729e_0
+  - ncurses=6.4=hcb278e6_0
+  - nest-asyncio=1.5.6=pyhd8ed1ab_0
+  - netcdf4=1.6.4=nompi_py310h6f5dce6_101
+  - numpy=1.25.1=py310ha4c1d20_0
+  - openjpeg=2.5.0=hfec8fc6_2
+  - openssl=3.1.1=hd590300_1
+  - orc=1.9.0=h385abfd_1
+  - packaging=23.1=pyhd8ed1ab_0
+  - pandas=2.0.3=py310h7cbd5c2_1
+  - parso=0.8.3=pyhd8ed1ab_0
+  - partd=1.4.0=pyhd8ed1ab_0
+  - pexpect=4.8.0=pyh1a96a4e_2
+  - pickleshare=0.7.5=py_1003
+  - pillow=10.0.0=py310h582fbeb_0
+  - pip=23.1.2=pyhd8ed1ab_0
+  - platformdirs=3.9.1=pyhd8ed1ab_0
+  - pluggy=1.2.0=pyhd8ed1ab_0
+  - prompt-toolkit=3.0.39=pyha770c72_0
+  - prompt_toolkit=3.0.39=hd8ed1ab_0
+  - psutil=5.9.5=py310h1fa729e_0
+  - pthread-stubs=0.4=h36c2ea0_1001
+  - ptyprocess=0.7.0=pyhd3deb0d_0
+  - pure_eval=0.2.2=pyhd8ed1ab_0
+  - pyarrow=12.0.1=py310h0576679_5_cpu
+  - pybind11-abi=4=hd8ed1ab_3
+  - pycosat=0.6.4=py310h5764c6d_1
+  - pycparser=2.21=pyhd8ed1ab_0
+  - pygments=2.15.1=pyhd8ed1ab_0
+  - pyopenssl=23.2.0=pyhd8ed1ab_1
+  - pysocks=1.7.1=pyha2e5f31_6
+  - python=3.10.12=hd12c33a_0_cpython
+  - python-dateutil=2.8.2=pyhd8ed1ab_0
+  - python-tzdata=2023.3=pyhd8ed1ab_0
+  - python_abi=3.10=3_cp310
+  - pytz=2023.3=pyhd8ed1ab_0
+  - pyyaml=6.0=py310h5764c6d_5
+  - pyzmq=25.1.0=py310h5bbb5d0_0
+  - rdma-core=28.9=h59595ed_1
+  - re2=2023.03.02=h8c504da_0
+  - readline=8.2=h8228510_1
+  - reproc=14.2.4=h0b41bf4_0
+  - reproc-cpp=14.2.4=hcb278e6_0
+  - requests=2.31.0=pyhd8ed1ab_0
+  - ruamel.yaml=0.17.32=py310h2372a71_0
+  - ruamel.yaml.clib=0.2.7=py310h1fa729e_1
+  - s2n=1.3.46=h06160fa_0
+  - setuptools=68.0.0=pyhd8ed1ab_0
+  - six=1.16.0=pyh6c4a22f_0
+  - snappy=1.1.10=h9fff704_0
+  - sortedcontainers=2.4.0=pyhd8ed1ab_0
+  - stack_data=0.6.2=pyhd8ed1ab_0
+  - tblib=1.7.0=pyhd8ed1ab_0
+  - tini=0.19.0=h166bdaf_1
+  - tk=8.6.12=h27826a3_0
+  - toolz=0.12.0=pyhd8ed1ab_0
+  - tornado=6.3.2=py310h2372a71_0
+  - tqdm=4.65.0=pyhd8ed1ab_1
+  - traitlets=5.9.0=pyhd8ed1ab_0
+  - typing-extensions=4.7.1=hd8ed1ab_0
+  - typing_extensions=4.7.1=pyha770c72_0
+  - tzdata=2023c=h71feb2d_0
+  - ucx=1.14.1=hf587318_2
+  - urllib3=2.0.3=pyhd8ed1ab_1
+  - wcwidth=0.2.6=pyhd8ed1ab_0
+  - wheel=0.40.0=pyhd8ed1ab_0
+  - xarray=2023.7.0=pyhd8ed1ab_0
+  - xorg-libxau=1.0.11=hd590300_0
+  - xorg-libxdmcp=1.1.3=h7f98852_0
+  - xz=5.2.6=h166bdaf_0
+  - yaml=0.2.5=h7f98852_2
+  - yaml-cpp=0.7.0=h27087fc_2
+  - yarl=1.9.2=py310h2372a71_0
+  - zeromq=4.3.4=h9c3ff4c_1
+  - zict=3.0.0=pyhd8ed1ab_0
+  - zipp=3.16.2=pyhd8ed1ab_0
+  - zstandard=0.19.0=py310h1275a96_2
+  - zstd=1.5.2=hfc55251_7
+prefix: /opt/conda

dockerfiles/minimal-notebook/notebooks/intro.ipynb → dockerfiles/minimal-notebook/notebooks/intro.ipynb.tpl

@@ -127,16 +127,29 @@
     "```\n",
     "> To enable this feature, remove the `.disable-local-data-shortcut` file.\n",
     "### Why is there a `intro.ipynb` in my home directory?\n",
-    "> This is the `Nimbus` introduction guide. It's provided to keep you updated on changes and provide access to an FAQ.\n",
-    "# Changelog\n",
-    "- Initial commit\n",
-    "- Adds nbgitpuller"
+    "> This is the `Nimbus` introduction guide. It's provided to keep you updated on changes and provide access to an FAQ."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "13b09108-ab94-4d02-8c42-b74c6631b3c8",
+   "metadata": {
+    "jupyter": {
+     "source_hidden": true
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "from IPython.display import Markdown, display\n",
+    "display(Markdown(\"/changelog.md\"))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2322f910-cd56-45db-909f-37457ac218f7",
    "metadata": {},
    "outputs": [],
    "source": []

dockerfiles/minimal-notebook/scripts/install-envs.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+mamba env update -n base -f /conda-envs/dask-gateway.yaml
+
+for env in $(find /conda-envs -type f -printf "%f\n"); do
+	name="${env%.*}"
+	mamba env create -n "${name}" -f "/conda-envs/${env}"
+	source /opt/conda/etc/profile.d/conda.sh
+	conda activate "${name}"
+	python -m ipykernel install --name="${name}"
+	conda deactivate
+done

dockerfiles/minimal-notebook/scripts/render-intro.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+jupyter nbconvert --execute --to notebook --stdout /notebooks/intro.ipynb.tpl > /notebooks/intro.ipynb

dockerfiles/minimal-notebook/tbump.toml

@@ -1,5 +1,5 @@
 [version]
-current = "0.1.7"
+current = "0.1.8"
 
 regex = '''
   (?P<major>\d+)