From 106d8415c3026dcba84ae1ad2f0f4634e80f32b4 Mon Sep 17 00:00:00 2001 From: Zhi-Jie Cao Date: Fri, 25 Aug 2023 15:43:01 +0800 Subject: [PATCH] Env fix --- README.md | 11 ++++-- conda.yaml | 101 +++++++++++++++++++++++++++++++++++++++++------------ 2 files changed, 86 insertions(+), 26 deletions(-) diff --git a/README.md b/README.md index 33edf8d..09f87f6 100644 --- a/README.md +++ b/README.md @@ -31,10 +31,15 @@ mamba env export -p ./conda --no-build > conda.yaml > > We may also choose to remove the `name:` and `prefix:` lines from the exported > file to redact the trace of absolute paths, as well as to remove our -> "mypackage" entry which should be installed as a development version: +> "mypackage" entry which should be installed as a development version. Here +> I've also ignored os-specific entries to support multiple os, but that's +> unnecessary if you only aim for a single os like linux: > -> `mamba env export -p ./conda --no-build | grep -Ev '^name|^prefix|mypackage' > -> conda.yaml` +> ```sh +> mamba env export -p ./conda --no-build | grep -Ev '^name|^prefix|mypackage' | +> grep -Ev 'linux|pyobjc|lib|keyutils|openmp|sed|osx|clang|llvm|compiler-rt' > +> conda.yaml +> ``` ### Clone the environment on another machine diff --git a/conda.yaml b/conda.yaml index 46ffb00..278b503 100644 --- a/conda.yaml +++ b/conda.yaml @@ -2,6 +2,7 @@ channels: - bioconda - conda-forge dependencies: + - _r-mutex=1.0.1 - alabaster=0.7.13 - amply=0.1.6 - anyio=3.7.1 @@ -20,10 +21,13 @@ dependencies: - beautifulsoup4=4.12.2 - bleach=6.0.0 - brotli-python=1.0.9 + - bwidget=1.9.14 - bzip2=1.0.8 + - c-ares=1.19.1 - ca-certificates=2023.7.22 - cached-property=1.5.2 - cached_property=1.5.2 + - cairo=1.16.0 - cattrs=23.1.2 - certifi=2023.7.22 - cffi=1.15.1 @@ -39,34 +43,47 @@ dependencies: - configargparse=1.7 - connection_pool=0.0.3 - coverage=7.3.0 + - curl=8.2.1 - datrie=0.8.2 - debugpy=1.6.8 - decorator=5.1.1 - - defusedxml=0.7.1 - docutils=0.17.1 - dpath=2.1.6 - entrypoints=0.4 - esbonio=0.16.1 - exceptiongroup=1.1.3 - executing=1.2.0 + - expat=2.5.0 - flit=3.9.0 - flit-core=3.9.0 + - font-ttf-dejavu-sans-mono=2.37 + - font-ttf-inconsolata=3.000 + - font-ttf-source-code-pro=2.038 + - font-ttf-ubuntu=0.83 + - fontconfig=2.14.2 + - fonts-conda-ecosystem=1 + - fonts-conda-forge=1 - fqdn=1.5.1 + - freetype=2.12.1 + - fribidi=1.0.10 + - gettext=0.21.1 - gitdb=4.0.10 - gitpython=3.1.32 + - gmp=6.2.1 + - graphite2=1.3.13 + - gsl=2.7 + - harfbuzz=7.3.0 - humanfriendly=10.0 + - icu=72.1 - idna=3.4 - imagesize=1.4.1 - - importlib-metadata=6.8.0 - - importlib_metadata=6.8.0 - - importlib_resources=6.0.1 - iniconfig=2.0.0 - ipykernel=6.25.1 - ipython=8.14.0 + - isl=0.25 - isoduration=20.11.0 - jedi=0.19.0 - jinja2=3.1.2 - - joblib=1.3.2 - json5=0.9.14 - jsonpointer=2.0 - jsonschema=4.19.0 @@ -82,27 +99,17 @@ dependencies: - jupyterlab_pygments=0.2.2 - jupyterlab_server=2.24.0 - jupytext=1.15.0 - - libblas=3.9.0 - - libcblas=3.9.0 - - libcxx=16.0.6 - - libexpat=2.5.0 - - libffi=3.4.2 - - libgfortran=5.0.0 - - libgfortran5=12.3.0 - - liblapack=3.9.0 - - liblapacke=3.9.0 - - libopenblas=0.3.23 - - libsodium=1.0.18 - - libsqlite=3.42.0 - - libzlib=1.2.13 - - llvm-openmp=16.0.6 + - krb5=1.21.2 + - lerc=4.0.0 - lsprotocol=2023.0.0a2 + - make=4.3 - markdown-it-py=3.0.0 - markupsafe=2.1.3 - - matplotlib-inline=0.1.6 - mdit-py-plugins=0.4.0 - mdurl=0.1.0 - mistune=3.0.1 + - mpc=1.3.1 + - mpfr=4.2.0 - nbclient=0.8.0 - nbconvert-core=7.7.4 - nbformat=5.9.2 @@ -115,11 +122,14 @@ dependencies: - packaging=23.1 - pandas=2.0.3 - pandocfilters=1.5.0 + - pango=1.50.14 - parse=1.19.1 - parso=0.8.3 + - pcre2=10.40 - pexpect=4.8.0 - pickleshare=0.7.5 - pip=23.2.1 + - pixman=0.40.0 - pkgutil-resolve-name=1.3.10 - plac=1.3.5 - platformdirs=3.10.0 @@ -129,14 +139,13 @@ dependencies: - prompt-toolkit=3.0.39 - prompt_toolkit=3.0.39 - psutil=5.9.5 + - pthread-stubs=0.4 - ptyprocess=0.7.0 - pulp=2.7.0 - pure_eval=0.2.2 - pycparser=2.21 - pygls=1.0.2 - pygments=2.16.1 - - pyobjc-core=9.2 - - pyobjc-framework-cocoa=9.2 - pyparsing=3.1.1 - pysocks=1.7.1 - pyspellchecker=0.7.2 @@ -151,6 +160,45 @@ dependencies: - pytz=2023.3 - pyyaml=6.0.1 - pyzmq=25.1.1 + - r-base=4.3.1 + - r-cli=3.6.1 + - r-colorspace=2.1_0 + - r-crayon=1.5.2 + - r-dplyr=1.1.2 + - r-ellipsis=0.3.2 + - r-fansi=1.0.4 + - r-farver=2.1.1 + - r-generics=0.1.3 + - r-ggplot2=3.4.3 + - r-glue=1.6.2 + - r-gtable=0.3.4 + - r-isoband=0.2.7 + - r-labeling=0.4.2 + - r-lattice=0.21_8 + - r-lifecycle=1.0.3 + - r-magrittr=2.0.3 + - r-mass=7.3_60 + - r-matrix=1.6_1 + - r-mgcv=1.9_0 + - r-munsell=0.5.0 + - r-nlme=3.1_163 + - r-pillar=1.9.0 + - r-pkgconfig=2.0.3 + - r-plyr=1.8.8 + - r-r6=2.5.1 + - r-rcolorbrewer=1.1_3 + - r-rcpp=1.0.11 + - r-reshape2=1.4.4 + - r-rlang=1.1.1 + - r-scales=1.2.1 + - r-stringi=1.7.12 + - r-stringr=1.5.0 + - r-tibble=3.2.1 + - r-tidyselect=1.2.0 + - r-utf8=1.2.3 + - r-vctrs=0.6.3 + - r-viridislite=0.4.2 + - r-withr=2.5.0 - readline=8.2 - referencing=0.30.2 - requests=2.31.0 @@ -162,6 +210,7 @@ dependencies: - scipy=1.11.2 - send2trash=1.8.2 - setuptools=68.1.2 + - sigtool=0.1.3 - six=1.16.0 - smart_open=6.3.0 - smmap=3.0.5 @@ -182,11 +231,13 @@ dependencies: - stack_data=0.6.2 - stopit=1.1.2 - tabulate=0.9.0 + - tapi=1100.0.11 - terminado=0.17.1 - threadpoolctl=3.2.0 - throttler=1.2.2 - tinycss2=1.2.1 - tk=8.6.12 + - tktable=2.10 - toml=0.10.2 - tomli=2.0.1 - tomli-w=1.0.0 @@ -199,16 +250,20 @@ dependencies: - typing_utils=0.1.0 - tzdata=2023c - uri-template=1.3.0 - - urllib3=2.0.4 - wcwidth=0.2.6 - webcolors=1.13 - webencodings=0.5.1 - websocket-client=1.6.2 - wheel=0.41.2 - wrapt=1.15.0 + - xorg-kbproto=1.0.7 + - xorg-renderproto=0.11.1 + - xorg-xextproto=7.3.0 + - xorg-xproto=7.0.31 - xz=5.2.6 - yaml=0.2.5 - yte=1.5.1 - zeromq=4.3.4 - zipp=3.16.2 + - zstd=1.5.2 - pip: