diff --git a/Makefile b/Makefile index c5dfd31..6edba2d 100644 --- a/Makefile +++ b/Makefile @@ -8,7 +8,7 @@ test_r: $(DOCKERRUN) darribas/gds:${GDS_VERSION} start.sh jupyter nbconvert --to html --execute /home/jovyan/test/gds/check_r_stack.ipynb write_stacks: write_py_stack write_r_stack write_py_stack: - $(DOCKERRUN) darribas/gds_py:${GDS_VERSION} start.sh sh -c "conda list > /home/jovyan/test/gds_py/stack_py.txt" + $(DOCKERRUN) darribas/gds_py:${GDS_VERSION} start.sh bash -c "conda list -n gds > /home/jovyan/test/gds_py/stack_py.txt" $(DOCKERRUN) darribas/gds_py:${GDS_VERSION} start.sh sed -i '1iGDS version: ${GDS_VERSION}' /home/jovyan/test/gds_py/stack_py.txt $(DOCKERRUN) darribas/gds_py:${GDS_VERSION} start.sh python -c "import subprocess, pandas; fo=open('/home/jovyan/test/gds_py/stack_py.md', 'w'); fo.write(pandas.read_json(subprocess.check_output(['conda', 'list', '--json']).decode())[['name', 'version', 'build_string', 'channel']].to_markdown());fo.close()" $(DOCKERRUN) darribas/gds_py:${GDS_VERSION} start.sh sed -i "1s/^/\n/" /home/jovyan/test/gds_py/stack_py.md @@ -18,7 +18,7 @@ write_r_stack: $(DOCKERRUN) darribas/gds:${GDS_VERSION} start.sh Rscript -e "library(knitr); ip <- as.data.frame(installed.packages()[,c(1,3:4)]); fc <- file('/home/jovyan/test/gds/stack_r.md'); writeLines(kable(ip, format = 'markdown'), fc); close(fc);" $(DOCKERRUN) darribas/gds:${GDS_VERSION} start.sh sed -i "1s/^/\n/" /home/jovyan/test/gds/stack_r.md write_py_explicit: - $(DOCKERRUN) darribas/gds_py:${GDS_VERSION} start.sh sh -c "conda list --explicit > /home/jovyan/test/gds_py/stack_py_explicit.txt" + $(DOCKERRUN) darribas/gds_py:${GDS_VERSION} start.sh sh -c "conda list -n gds --explicit > /home/jovyan/test/gds_py/stack_py_explicit.txt" website_build: cd website && \ rm -rf _includes && \ diff --git a/gds_py/stack_py.txt b/gds_py/stack_py.txt index ea02d28..e1a0b07 100644 --- a/gds_py/stack_py.txt +++ b/gds_py/stack_py.txt @@ -1,203 +1,537 @@ GDS version: 10.0 -# packages in environment at /opt/conda: +# packages in environment at /opt/conda/envs/gds: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge -alembic 1.12.0 pyhd8ed1ab_0 conda-forge +access 1.1.8 pyhd8ed1ab_1 conda-forge +accessible-pygments 0.0.4 pyhd8ed1ab_0 conda-forge +affine 2.4.0 pyhd8ed1ab_0 conda-forge +alabaster 0.7.13 pyhd8ed1ab_0 conda-forge +amply 0.1.6 pyhd8ed1ab_0 conda-forge +annotated-types 0.6.0 pyhd8ed1ab_0 conda-forge anyio 4.0.0 pyhd8ed1ab_0 conda-forge +appdirs 1.4.4 pyh9f0ad1d_0 conda-forge argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge -argon2-cffi-bindings 21.2.0 py311h459d7ec_4 conda-forge +argon2-cffi-bindings 21.2.0 py39hd1e30aa_4 conda-forge +arpack 3.8.0 nompi_h0baa96a_101 conda-forge arrow 1.3.0 pyhd8ed1ab_0 conda-forge asttokens 2.4.0 pyhd8ed1ab_0 conda-forge async-lru 2.0.4 pyhd8ed1ab_0 conda-forge -async_generator 1.10 py_0 conda-forge attrs 23.1.0 pyh71513ae_1 conda-forge +aws-c-auth 0.7.4 h1083cbe_2 conda-forge +aws-c-cal 0.6.2 h09139f6_2 conda-forge +aws-c-common 0.9.3 hd590300_0 conda-forge +aws-c-compression 0.2.17 h184a658_3 conda-forge +aws-c-event-stream 0.3.2 h6fea174_2 conda-forge +aws-c-http 0.7.13 hb59894b_2 conda-forge +aws-c-io 0.13.33 h161b759_0 conda-forge +aws-c-mqtt 0.9.7 h55cd26b_0 conda-forge +aws-c-s3 0.3.18 hfb4bb88_0 conda-forge +aws-c-sdkutils 0.1.12 h184a658_2 conda-forge +aws-checksums 0.1.17 h184a658_2 conda-forge +aws-crt-cpp 0.24.3 h0770d84_1 conda-forge +aws-sdk-cpp 1.11.156 h10f61e1_5 conda-forge babel 2.13.0 pyhd8ed1ab_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.2 pyha770c72_0 conda-forge +black 23.10.0 py39hf3d152e_0 conda-forge bleach 6.1.0 pyhd8ed1ab_0 conda-forge -blinker 1.6.3 pyhd8ed1ab_0 conda-forge -boltons 23.0.0 pyhd8ed1ab_0 conda-forge -brotli-python 1.1.0 py311hb755f60_1 conda-forge +blosc 1.21.5 h0f2a231_0 conda-forge +bokeh 3.3.0 pyhd8ed1ab_0 conda-forge +boto3 1.28.66 pyhd8ed1ab_0 conda-forge +botocore 1.31.66 pyhd8ed1ab_0 conda-forge +bottleneck 1.3.7 py39h44dd56e_1 conda-forge +branca 0.6.0 pyhd8ed1ab_0 conda-forge +brotli 1.1.0 hd590300_1 conda-forge +brotli-bin 1.1.0 hd590300_1 conda-forge +brotli-python 1.1.0 py39h3d6467e_1 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.20.1 hd590300_0 conda-forge +c-blosc2 2.10.5 hb4ffafa_0 conda-forge ca-certificates 2023.7.22 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge +cachetools 5.3.1 pyhd8ed1ab_0 conda-forge +cairo 1.18.0 h3faef2a_0 conda-forge +cenpy 1.0.1 pyhd8ed1ab_0 conda-forge certifi 2023.7.22 pyhd8ed1ab_0 conda-forge -certipy 0.1.3 py_0 conda-forge -cffi 1.16.0 py311hb3a22ac_0 conda-forge +cffi 1.16.0 py39h7a31438_0 conda-forge +cfitsio 4.3.0 hbdc6101_0 conda-forge +cftime 1.6.2 py39h44dd56e_2 conda-forge charset-normalizer 3.3.0 pyhd8ed1ab_0 conda-forge +click 8.1.7 unix_pyh707e725_0 conda-forge +click-plugins 1.1.1 py_0 conda-forge +cligj 0.7.2 pyhd8ed1ab_1 conda-forge +cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge +clustergram 0.8.0 pyhd8ed1ab_1 conda-forge +coin-or-cbc 2.10.10 h9002f0b_0 conda-forge +coin-or-cgl 0.60.7 h516709c_0 conda-forge +coin-or-clp 1.17.8 h1ee7a9c_0 conda-forge +coin-or-osi 0.108.8 ha2443b9_0 conda-forge +coin-or-utils 2.11.9 hee58242_0 conda-forge +coincbc 2.10.10 0_metapackage conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge +colorcet 3.0.1 pyhd8ed1ab_0 conda-forge comm 0.1.4 pyhd8ed1ab_0 conda-forge -conda 23.9.0 py311h38be061_0 conda-forge -conda-package-handling 2.2.0 pyh38be061_0 conda-forge -conda-package-streaming 0.9.0 pyhd8ed1ab_0 conda-forge -configurable-http-proxy 4.5.6 h92b4e83_1 conda-forge -cryptography 41.0.4 py311h63ff55d_0 conda-forge -debugpy 1.8.0 py311hb755f60_1 conda-forge +contextily 1.4.0 pyhd8ed1ab_0 conda-forge +contourpy 1.1.1 py39h7633fee_1 conda-forge +coverage 7.3.2 pypi_0 pypi +cubo 2023.7.2 pyhd8ed1ab_0 conda-forge +cycler 0.12.1 pyhd8ed1ab_0 conda-forge +cython 3.0.4 py39h3d6467e_0 conda-forge +cytoolz 0.12.2 py39hd1e30aa_1 conda-forge +dask 2023.10.0 pyhd8ed1ab_0 conda-forge +dask-core 2023.10.0 pyhd8ed1ab_0 conda-forge +dask-geopandas 0.3.1 pyhd8ed1ab_1 conda-forge +dataclasses 0.8 pyhc8e2a94_3 conda-forge +datashader 0.15.2 pyhd8ed1ab_0 conda-forge +datashape 0.5.4 py_1 conda-forge +debugpy 1.8.0 py39h3d6467e_1 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge +deprecation 2.1.0 pyh9f0ad1d_0 conda-forge +descartes 1.1.0 py_4 conda-forge +distributed 2023.10.0 pyhd8ed1ab_0 conda-forge +docutils 0.18.1 py39hf3d152e_1 conda-forge +emcee 3.1.4 pyhd8ed1ab_0 conda-forge entrypoints 0.4 pyhd8ed1ab_0 conda-forge +esda 2.5.0 pyhd8ed1ab_0 conda-forge +et_xmlfile 1.1.0 pyhd8ed1ab_0 conda-forge exceptiongroup 1.1.3 pyhd8ed1ab_0 conda-forge executing 1.2.0 pyhd8ed1ab_0 conda-forge -fmt 10.1.1 h00ab1b0_0 conda-forge +expat 2.5.0 hcb278e6_1 conda-forge +fiona 1.9.5 py39h01ac8ae_0 conda-forge +flake8 6.1.0 pyhd8ed1ab_0 conda-forge +folium 0.14.0 pyhd8ed1ab_0 conda-forge +font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge +font-ttf-inconsolata 3.000 h77eed37_0 conda-forge +font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge +font-ttf-ubuntu 0.83 hab24e00_0 conda-forge +fontconfig 2.14.2 h14ed4e7_0 conda-forge +fonts-conda-ecosystem 1 0 conda-forge +fonts-conda-forge 1 0 conda-forge +fonttools 4.43.1 py39hd1e30aa_0 conda-forge fqdn 1.5.1 pyhd8ed1ab_0 conda-forge +freetype 2.12.1 h267a509_2 conda-forge +freexl 2.0.0 h743c826_0 conda-forge +fsspec 2023.9.2 pyh1a96a4e_0 conda-forge +fuzzywuzzy 0.18.0 pyhd8ed1ab_0 conda-forge +gdal 3.7.2 py39h41b90d8_7 conda-forge +geoalchemy2 0.14.1 pyhd8ed1ab_0 conda-forge +geocube 0.4.2 pyhd8ed1ab_1 conda-forge +geographiclib 1.52 pyhd8ed1ab_0 conda-forge +geojson 3.0.1 pyhd8ed1ab_0 conda-forge +geopandas 0.14.0 pyhd8ed1ab_1 conda-forge +geopandas-base 0.14.0 pyha770c72_1 conda-forge +geopy 2.4.0 pyhd8ed1ab_0 conda-forge +geos 3.12.0 h59595ed_0 conda-forge +geotiff 1.7.1 hf074850_14 conda-forge +gettext 0.21.1 h27087fc_0 conda-forge +gflags 2.2.2 he1b5a44_1004 conda-forge +giddy 2.3.4 pyhd8ed1ab_1 conda-forge +giflib 5.2.1 h0b41bf4_3 conda-forge +glog 0.6.0 h6f12383_0 conda-forge +glpk 5.0 h445213a_0 conda-forge gmp 6.2.1 h58526e2_0 conda-forge -greenlet 3.0.0 py311hb755f60_1 conda-forge +gmpy2 2.1.2 py39h376b7d2_1 conda-forge +gpxpy 1.5.0 pyhd8ed1ab_0 conda-forge +greenlet 3.0.0 py39h3d6467e_1 conda-forge +gstools 1.5.0 py39hddac248_1 conda-forge +h3-py 3.7.6 py39h3d6467e_1 conda-forge +h5py 3.10.0 nompi_py39h87cadad_100 conda-forge +hankel 1.2.2 pyhd8ed1ab_0 conda-forge +hdbscan 0.8.33 py39h44dd56e_4 conda-forge +hdf4 4.2.15 h2a13503_7 conda-forge +hdf5 1.14.2 nompi_h4f84152_100 conda-forge +hilbertcurve 2.0.5 pyhd8ed1ab_0 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge +imagesize 1.4.1 pyhd8ed1ab_0 conda-forge importlib-metadata 6.8.0 pyha770c72_0 conda-forge +importlib-resources 6.1.0 pyhd8ed1ab_0 conda-forge importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge importlib_resources 6.1.0 pyhd8ed1ab_0 conda-forge +inequality 1.0.0 pyhd8ed1ab_1 conda-forge +iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge ipykernel 6.25.2 pyh2140261_0 conda-forge +ipyleaflet 0.17.4 pyhd8ed1ab_0 conda-forge +ipympl 0.9.3 pyhd8ed1ab_0 conda-forge +ipyspin 1.0.1 pyhd8ed1ab_0 conda-forge ipython 8.16.1 pyh0d859eb_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge +ipyurl 0.1.2 pyh3684270_1 conda-forge +ipywidgets 8.1.1 pyhd8ed1ab_0 conda-forge isoduration 20.11.0 pyhd8ed1ab_0 conda-forge jedi 0.19.1 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge +jmespath 1.0.1 pyhd8ed1ab_0 conda-forge +joblib 1.3.2 pyhd8ed1ab_0 conda-forge +json-c 0.17 h7ab15ed_0 conda-forge json5 0.9.14 pyhd8ed1ab_0 conda-forge -jsonpatch 1.33 pyhd8ed1ab_0 conda-forge -jsonpointer 2.4 py311h38be061_3 conda-forge +jsonpointer 2.4 py39hf3d152e_3 conda-forge jsonschema 4.19.1 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.7.1 pyhd8ed1ab_0 conda-forge jsonschema-with-format-nongpl 4.19.1 pyhd8ed1ab_0 conda-forge +jupyter-book 0.15.1 pyhd8ed1ab_0 conda-forge +jupyter-cache 0.6.1 pyhd8ed1ab_0 conda-forge jupyter-lsp 2.2.0 pyhd8ed1ab_0 conda-forge +jupyter_bokeh 2.0.4 pyhd8ed1ab_0 conda-forge jupyter_client 8.4.0 pyhd8ed1ab_0 conda-forge -jupyter_core 5.4.0 py311h38be061_0 conda-forge +jupyter_core 5.4.0 py39hf3d152e_0 conda-forge jupyter_events 0.8.0 pyhd8ed1ab_0 conda-forge jupyter_server 2.8.0 pyhd8ed1ab_0 conda-forge jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge -jupyter_telemetry 0.1.0 pyhd8ed1ab_1 conda-forge -jupyterhub 4.0.2 pyh31011fe_0 conda-forge -jupyterhub-base 4.0.2 pyh31011fe_0 conda-forge +jupyter_server_xarray_leaflet 0.2.3 pyhd8ed1ab_0 conda-forge jupyterlab 4.0.7 pyhd8ed1ab_0 conda-forge +jupyterlab-geojson 3.4.0 pypi_0 pypi +jupyterlab-myst 2.1.0 pypi_0 pypi jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge jupyterlab_server 2.25.0 pyhd8ed1ab_0 conda-forge +jupyterlab_widgets 3.0.9 pyhd8ed1ab_0 conda-forge +jupytext 1.15.2 pyh5da7574_0 conda-forge +kealib 1.5.2 hcd42e92_1 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge +kiwisolver 1.4.5 py39h7633fee_1 conda-forge krb5 1.21.2 h659d440_0 conda-forge +latexcodec 2.0.1 pyh9f0ad1d_0 conda-forge +lcms2 2.15 hb7c19ff_3 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge +legendgram 0.0.3 py_1 conda-forge +lerc 4.0.0 h27087fc_0 conda-forge +levenshtein 0.23.0 py39h3d6467e_0 conda-forge +libabseil 20230802.1 cxx17_h59595ed_0 conda-forge +libaec 1.1.2 h59595ed_1 conda-forge libarchive 3.7.2 h039dbb9_0 conda-forge +libarrow 10.0.1 h8d17fec_48_cpu conda-forge +libblas 3.9.0 19_linux64_openblas conda-forge +libboost-headers 1.82.0 ha770c72_6 conda-forge +libbrotlicommon 1.1.0 hd590300_1 conda-forge +libbrotlidec 1.1.0 hd590300_1 conda-forge +libbrotlienc 1.1.0 hd590300_1 conda-forge +libcblas 3.9.0 19_linux64_openblas conda-forge +libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcurl 8.4.0 hca28451_0 conda-forge +libdeflate 1.19 hd590300_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge +libevent 2.1.12 hf998b51_1 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.2.0 h807b86a_2 conda-forge +libgdal 3.7.2 h6f3d308_7 conda-forge +libgdal-arrow-parquet 3.7.2 h5eff638_7 conda-forge +libgfortran-ng 13.2.0 h69a702a_2 conda-forge +libgfortran5 13.2.0 ha4646dd_2 conda-forge +libglib 2.78.0 hebfc3b9_0 conda-forge libgomp 13.2.0 h807b86a_2 conda-forge +libgoogle-cloud 2.12.0 h19a6dae_3 conda-forge +libgrpc 1.58.1 he06187c_2 conda-forge libiconv 1.17 h166bdaf_0 conda-forge -libmamba 1.5.2 had39da4_0 conda-forge -libmambapy 1.5.2 py311hf2555c7_0 conda-forge +libjpeg-turbo 3.0.0 hd590300_1 conda-forge +libkml 1.3.0 h01aab08_1018 conda-forge +liblapack 3.9.0 19_linux64_openblas conda-forge +liblapacke 3.9.0 19_linux64_openblas conda-forge +libllvm14 14.0.6 hcd5def8_4 conda-forge +libnetcdf 4.9.2 nompi_h80fb2b6_112 conda-forge libnghttp2 1.52.0 h61bc06f_0 conda-forge libnsl 2.0.1 hd590300_0 conda-forge +libnuma 2.0.16 h0b41bf4_1 conda-forge +libopenblas 0.3.24 pthreads_h413a1c8_0 conda-forge +libpng 1.6.39 h753d276_0 conda-forge +libpq 16.0 hfc447b1_1 conda-forge +libprotobuf 4.24.3 hf27288f_1 conda-forge +libpysal 4.8.0 pyhd8ed1ab_1 conda-forge +libre2-11 2023.06.02 h7a70373_0 conda-forge +librttopo 1.1.0 hb58d41b_14 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge -libsolv 0.7.25 hfc55251_0 conda-forge +libspatialindex 1.9.3 h9c3ff4c_4 conda-forge +libspatialite 5.1.0 h090f1da_0 conda-forge libsqlite 3.43.2 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_2 conda-forge +libthrift 0.19.0 hb90f79a_1 conda-forge +libtiff 4.6.0 ha9c0a0a_2 conda-forge +libutf8proc 2.8.0 h166bdaf_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge -libuv 1.46.0 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