Env fix

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
 

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: