pypsa-usa
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PyPSA
snakemake error when spinning up new environment
Checklist
- [x] I am using the current
masterbranch - [x] I am running on an up-to-date
pypsa-usaenvironment. Update viaconda env update -f envs/environment.yaml
The Issue
HI All,
I have been struggling to get past this issue for over 3 months now. I've tried everything.
So this morning I tried to spin up a brand new environment. When I try to run the slurm script, I get these errors
Restricted license - for non-production use only - expires 2025-11-24
/home/jaclynr6/.conda/envs/pypsa-usa-test/lib/python3.11/site-packages/pulp/apis/gurobi_api.py:170: UserWarning: GUROBI error: Unknown parameter '_test'.
warnings.warn("GUROBI error: {}.".format(e))
Traceback (most recent call last):
File "/home/jaclynr6/.conda/envs/pypsa-usa-test/bin/snakemake", line 10, in <module>
sys.exit(main())
^^^^^^
File "/home/jaclynr6/.conda/envs/pypsa-usa-test/lib/python3.11/site-packages/snakemake/__init__.py", line 3141, in main
success = snakemake(
^^^^^^^^^^
TypeError: snakemake() got an unexpected keyword argument 'listrules'
Please help me.. I'm about to give up :(
Steps To Reproduce
Follow the steps in the documentation https://pypsa-usa.readthedocs.io/en/latest/about-install.html
Then try to bash the slurm script.
Expected Behavior
I am able to get past this snakemake issue
Error Message
Restricted license - for non-production use only - expires 2025-11-24
/home/jaclynr6/.conda/envs/pypsa-usa-test/lib/python3.11/site-packages/pulp/apis/gurobi_api.py:170: UserWarning: GUROBI error: Unknown parameter '_test'.
warnings.warn("GUROBI error: {}.".format(e))
Traceback (most recent call last):
File "/home/jaclynr6/.conda/envs/pypsa-usa-test/bin/snakemake", line 10, in <module>
sys.exit(main())
^^^^^^
File "/home/jaclynr6/.conda/envs/pypsa-usa-test/lib/python3.11/site-packages/snakemake/__init__.py", line 3141, in main
success = snakemake(
^^^^^^^^^^
TypeError: snakemake() got an unexpected keyword argument 'listrules'
conda list
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
affine 2.4.0 pyhd8ed1ab_1 conda-forge
aioeasywebdav 2.4.0 pyha770c72_0 conda-forge
aiohappyeyeballs 2.6.1 pyhd8ed1ab_0 conda-forge
aiohttp 3.11.16 py311h2dc5d0c_0 conda-forge
aiosignal 1.3.2 pyhd8ed1ab_0 conda-forge
alsa-lib 1.2.11 hd590300_1 conda-forge
ampl-asl 1.0.0 h5888daf_2 conda-forge
amply 0.1.6 pyhd8ed1ab_1 conda-forge
annotated-types 0.7.0 pyhd8ed1ab_1 conda-forge
anyio 4.9.0 pyh29332c3_0 conda-forge
appdirs 1.4.4 pyhd8ed1ab_1 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_1 conda-forge
argon2-cffi-bindings 21.2.0 py311h9ecbd09_5 conda-forge
arrow 1.3.0 pyhd8ed1ab_1 conda-forge
asttokens 3.0.0 pyhd8ed1ab_1 conda-forge
async-lru 2.0.5 pyh29332c3_0 conda-forge
atk-1.0 2.38.0 hd4edc92_1 conda-forge
atlite 0.3.0 pyhd8ed1ab_1 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 25.3.0 pyh71513ae_0 conda-forge
aws-c-auth 0.8.0 hb88c0a9_10 conda-forge
aws-c-cal 0.8.0 hecf86a2_2 conda-forge
aws-c-common 0.10.3 hb9d3cd8_0 conda-forge
aws-c-compression 0.3.0 hf42f96a_2 conda-forge
aws-c-event-stream 0.5.0 h1ffe551_7 conda-forge
aws-c-http 0.9.1 hab05fe4_2 conda-forge
aws-c-io 0.15.2 hdeadb07_2 conda-forge
aws-c-mqtt 0.11.0 h7bd072d_8 conda-forge
aws-c-s3 0.7.4 h3a84f74_0 conda-forge
aws-c-sdkutils 0.2.1 hf42f96a_1 conda-forge
aws-checksums 0.2.2 hf42f96a_1 conda-forge
aws-crt-cpp 0.29.6 h159bff8_2 conda-forge
aws-sdk-cpp 1.11.458 h5558e3c_0 conda-forge
azure-core-cpp 1.14.0 h5cfcd09_0 conda-forge
azure-identity-cpp 1.10.0 h113e628_0 conda-forge
azure-storage-blobs-cpp 12.13.0 h3cf044e_1 conda-forge
azure-storage-common-cpp 12.8.0 h736e048_1 conda-forge
azure-storage-files-datalake-cpp 12.12.0 ha633028_1 conda-forge
babel 2.17.0 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
bcrypt 4.3.0 py311h9e33e62_0 conda-forge
beautifulsoup4 4.13.3 pyha770c72_0 conda-forge
bleach 6.2.0 pyh29332c3_4 conda-forge
bleach-with-css 6.2.0 h82add2a_4 conda-forge
blosc 1.21.6 hef167b5_0 conda-forge
bokeh 3.7.2 pyhd8ed1ab_1 conda-forge
boto3 1.37.28 pyhd8ed1ab_0 conda-forge
botocore 1.37.28 pyge310_1234567_0 conda-forge
bottleneck 1.4.2 py311h9f3472d_0 conda-forge
branca 0.8.1 pyhd8ed1ab_0 conda-forge
brotli 1.1.0 hb9d3cd8_2 conda-forge
brotli-bin 1.1.0 hb9d3cd8_2 conda-forge
brotli-python 1.1.0 py311hfdbb021_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.4 hb9d3cd8_0 conda-forge
c-blosc2 2.12.0 hb4ffafa_0 conda-forge
ca-certificates 2025.1.31 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.5.2 pyhd8ed1ab_0 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
cartopy 0.23.0 py311h7db5c69_2 conda-forge
cdsapi 0.7.5 pyhd8ed1ab_1 conda-forge
certifi 2025.1.31 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py311hf29c0ef_0 conda-forge
cfitsio 4.3.1 hbdc6101_0 conda-forge
cftime 1.6.4 py311h9f3472d_1 conda-forge
charset-normalizer 3.4.1 pyhd8ed1ab_0 conda-forge
click 8.1.8 pyh707e725_0 conda-forge
click-plugins 1.1.1 pyhd8ed1ab_1 conda-forge
cligj 0.7.2 pyhd8ed1ab_2 conda-forge
cloudpickle 3.1.1 pyhd8ed1ab_0 conda-forge
coin-or-cbc 2.10.12 h00e76a6_2 conda-forge
coin-or-cgl 0.60.9 h82e2f02_4 conda-forge
coin-or-clp 1.17.10 h8a7a1e7_1 conda-forge
coin-or-osi 0.108.11 h96cc833_4 conda-forge
coin-or-utils 2.11.12 h3a12e53_2 conda-forge
coincbc 2.10.12 2_metapackage conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
coloredlogs 15.0.1 pyhd8ed1ab_4 conda-forge
comm 0.2.2 pyhd8ed1ab_1 conda-forge
configargparse 1.7 pyhd8ed1ab_1 conda-forge
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
contourpy 1.3.1 py311hd18a35c_0 conda-forge
country_converter 1.0.0 pyhd8ed1ab_1 conda-forge
countrycode 0.4.0 pypi_0 pypi
cryptography 44.0.2 py311hafd3f86_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
cyipopt 1.5.0 py311h3e7193c_3 conda-forge
cytoolz 1.0.1 py311h9ecbd09_0 conda-forge
dask 2025.3.0 pyhd8ed1ab_0 conda-forge
dask-core 2025.3.0 pyhd8ed1ab_0 conda-forge
datapi 0.3.1 pyhd8ed1ab_0 conda-forge
datrie 0.8.2 py311h9ecbd09_8 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
debugpy 1.8.13 py311hfdbb021_0 conda-forge
decorator 5.2.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
deprecation 2.1.0 pyh9f0ad1d_0 conda-forge
descartes 1.1.0 pyhd8ed1ab_5 conda-forge
dill 0.3.9 pypi_0 pypi
distributed 2025.3.0 pyhd8ed1ab_0 conda-forge
distro 1.9.0 pyhd8ed1ab_1 conda-forge
docutils 0.21.2 pyhd8ed1ab_1 conda-forge
dpath 2.2.0 pyha770c72_0 conda-forge
dropbox 12.0.2 pyhd8ed1ab_1 conda-forge
duckdb 0.10.0 pypi_0 pypi
eido 0.2.4 pyhd8ed1ab_0 conda-forge
et_xmlfile 2.0.0 pyhd8ed1ab_1 conda-forge
exceptiongroup 1.2.2 pyhd8ed1ab_1 conda-forge
executing 2.1.0 pyhd8ed1ab_1 conda-forge
expat 2.7.0 h5888daf_0 conda-forge
filechunkio 1.8 py_2 conda-forge
fiona 1.10.1 pypi_0 pypi
flake8 7.2.0 pypi_0 pypi
folium 0.19.5 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 h77eed37_3 conda-forge
fontconfig 2.15.0 h7e30c49_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.57.0 py311h2dc5d0c_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_1 conda-forge
freetype 2.13.3 h48d6fc4_0 conda-forge
freexl 2.0.0 h9dce30a_2 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
frozenlist 1.5.0 py311h2dc5d0c_1 conda-forge
fs 2.4.11 pyhd8ed1ab_3 conda-forge
fsspec 2025.3.2 pyhd8ed1ab_0 conda-forge
ftputil 5.1.0 pyhd8ed1ab_0 conda-forge
gdal 3.7.3 py311h39b4e0e_11 conda-forge
gdk-pixbuf 2.42.10 h829c605_5 conda-forge
geographiclib 1.52 pyhd8ed1ab_0 conda-forge
geopandas 1.0.1 pyhd8ed1ab_3 conda-forge
geopandas-base 1.0.1 pyha770c72_3 conda-forge
geopy 2.4.0 pyhd8ed1ab_0 conda-forge
geos 3.12.1 h59595ed_0 conda-forge
geotiff 1.7.1 hf074850_14 conda-forge
gettext 0.23.1 h5888daf_0 conda-forge
gettext-tools 0.23.1 h5888daf_0 conda-forge
gflags 2.2.2 h5888daf_1005 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
gitdb 4.0.12 pyhd8ed1ab_0 conda-forge
gitpython 3.1.44 pyhff2d567_0 conda-forge
glib 2.78.4 hfc55251_0 conda-forge
glib-tools 2.78.4 hfc55251_0 conda-forge
glog 0.7.1 hbabe93e_0 conda-forge
google-api-core 2.24.2 pyhd8ed1ab_0 conda-forge
google-api-python-client 2.165.0 pyhff2d567_0 conda-forge
google-auth 2.38.0 pyhd8ed1ab_0 conda-forge
google-auth-httplib2 0.2.0 pyhd8ed1ab_1 conda-forge
google-cloud-core 2.4.3 pyhd8ed1ab_0 conda-forge
google-cloud-storage 3.1.0 pyhd8ed1ab_0 conda-forge
google-crc32c 1.7.1 py311h0973507_0 conda-forge
google-resumable-media 2.7.2 pyhd8ed1ab_2 conda-forge
googleapis-common-protos 1.69.2 pyhd8ed1ab_0 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
graphviz 9.0.0 h78e8752_1 conda-forge
grpcio 1.67.1 py311h9c9ff8c_0 conda-forge
gst-plugins-base 1.22.9 h8e1006c_0 conda-forge
gstreamer 1.22.9 h98fc4e7_0 conda-forge
gtk2 2.24.33 h280cfa0_4 conda-forge
gts 0.7.6 h977cf35_4 conda-forge
gurobi 11.0.3 py311_0 gurobi
h2 4.2.0 pyhd8ed1ab_0 conda-forge
harfbuzz 8.3.0 h3d44ed6_0 conda-forge
hdf4 4.2.15 h2a13503_7 conda-forge
hdf5 1.14.3 nompi_h2d575fe_109 conda-forge
highspy 1.10.0 pypi_0 pypi
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
httplib2 0.22.0 pyhd8ed1ab_1 conda-forge
humanfriendly 10.0 pyh707e725_8 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
importlib-metadata 8.6.1 pyha770c72_0 conda-forge
importlib_metadata 8.6.1 hd8ed1ab_0 conda-forge
importlib_resources 6.5.2 pyhd8ed1ab_0 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_1 conda-forge
ipopt 3.14.17 h59d4785_0 conda-forge
ipykernel 6.25.2 pyh2140261_0 conda-forge
ipython 8.16.1 pyh0d859eb_0 conda-forge
ipywidgets 8.1.5 pyhd8ed1ab_1 conda-forge
isoduration 20.11.0 pyhd8ed1ab_1 conda-forge
jedi 0.19.2 pyhd8ed1ab_1 conda-forge
jinja2 3.1.6 pyhd8ed1ab_0 conda-forge
jmespath 1.0.1 pyhd8ed1ab_1 conda-forge
joblib 1.4.2 pyhd8ed1ab_1 conda-forge
json-c 0.17 h1220068_1 conda-forge
json5 0.12.0 pyhd8ed1ab_0 conda-forge
jsonpointer 3.0.0 py311h38be061_1 conda-forge
jsonschema 4.23.0 pyhd8ed1ab_1 conda-forge
jsonschema-specifications 2024.10.1 pyhd8ed1ab_1 conda-forge
jsonschema-with-format-nongpl 4.23.0 hd8ed1ab_1 conda-forge
jupyter 1.0.0 pyhd8ed1ab_10 conda-forge
jupyter-lsp 2.2.5 pyhd8ed1ab_1 conda-forge
jupyter_client 8.6.3 pyhd8ed1ab_1 conda-forge
jupyter_console 6.6.3 pyhd8ed1ab_1 conda-forge
jupyter_core 5.7.2 pyh31011fe_1 conda-forge
jupyter_events 0.12.0 pyh29332c3_0 conda-forge
jupyter_server 2.15.0 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.5.3 pyhd8ed1ab_1 conda-forge
jupyterlab 4.0.13 pyhd8ed1ab_1 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_2 conda-forge
jupyterlab_server 2.27.3 pyhd8ed1ab_1 conda-forge
jupyterlab_widgets 3.0.13 pyhd8ed1ab_1 conda-forge
kaleido 0.2.1 pypi_0 pypi
kealib 1.5.3 hf8d3e68_2 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.7 py311hd18a35c_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20240722.0 cxx17_hbbce691_4 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libarchive 3.7.4 hfca40fe_0 conda-forge
libarrow 16.1.0 h5847d97_47_cpu conda-forge
libarrow-acero 16.1.0 hf256b9d_47_cpu conda-forge
libarrow-dataset 16.1.0 hf256b9d_47_cpu conda-forge
libarrow-substrait 16.1.0 he72799e_47_cpu conda-forge
libasprintf 0.23.1 h8e693c7_0 conda-forge
libasprintf-devel 0.23.1 h8e693c7_0 conda-forge
libblas 3.9.0 20_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hb9d3cd8_2 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_2 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_2 conda-forge
libcap 2.71 h39aace5_0 conda-forge
libcblas 3.9.0 20_linux64_openblas conda-forge
libclang 15.0.7 default_h127d8a8_5 conda-forge
libclang13 15.0.7 default_h5d6823c_5 conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.13.0 h332b0f4_0 conda-forge
libdeflate 1.19 hd590300_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.7.0 h5888daf_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc 14.2.0 h767d61c_2 conda-forge
libgcc-ng 14.2.0 h69a702a_2 conda-forge
libgcrypt-lib 1.11.0 hb9d3cd8_2 conda-forge
libgd 2.3.3 h119a65a_9 conda-forge
libgdal 3.7.3 h184a269_11 conda-forge
libgettextpo 0.23.1 h5888daf_0 conda-forge
libgettextpo-devel 0.23.1 h5888daf_0 conda-forge
libgfortran 14.2.0 h69a702a_2 conda-forge
libgfortran-ng 14.2.0 h69a702a_2 conda-forge
libgfortran5 14.2.0 hf1ad2bd_2 conda-forge
libglib 2.78.4 h783c2da_0 conda-forge
libgomp 14.2.0 h767d61c_2 conda-forge
libgoogle-cloud 2.31.0 h804f50b_0 conda-forge
libgoogle-cloud-storage 2.31.0 h0121fbd_0 conda-forge
libgpg-error 1.51 hbd13f7d_1 conda-forge
libgrpc 1.67.1 hc2c308b_0 conda-forge
libhwloc 2.11.2 default_he43201b_1000 conda-forge
libiconv 1.18 h4ce23a2_1 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
libkml 1.3.0 hf539b9f_1021 conda-forge
liblapack 3.9.0 20_linux64_openblas conda-forge
liblapacke 3.9.0 20_linux64_openblas conda-forge
libllvm15 15.0.7 hb3ce162_4 conda-forge
liblzma 5.8.1 hb9d3cd8_0 conda-forge
liblzma-devel 5.8.1 hb9d3cd8_0 conda-forge
libnetcdf 4.9.2 nompi_h135f659_114 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.5 h4ab18f5_0 conda-forge
libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libparquet 16.1.0 h9f9be6e_47_cpu conda-forge
libpng 1.6.47 h943b412_0 conda-forge
libpq 16.4 h2d7952a_3 conda-forge
libprotobuf 5.28.2 h5b01275_0 conda-forge
libre2-11 2024.07.02 hbbce691_2 conda-forge
librsvg 2.56.3 he3f83f7_1 conda-forge
librttopo 1.1.0 h8917695_15 conda-forge
libscotch 7.0.4 h2fe6a88_5 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsodium 1.0.20 h4ab18f5_0 conda-forge
libspatialite 5.1.0 h72606ae_3 conda-forge
libspral 2024.05.08 h2b245be_4 conda-forge
libsqlite 3.49.1 hee588c1_2 conda-forge
libssh2 1.11.1 hf672d98_0 conda-forge
libstdcxx 14.2.0 h8f9b012_2 conda-forge
libstdcxx-ng 14.2.0 h4852527_2 conda-forge
libsystemd0 256.9 h2774228_0 conda-forge
libthrift 0.21.0 h0e7cc3e_0 conda-forge
libtiff 4.6.0 ha9c0a0a_2 conda-forge
libutf8proc 2.9.0 hb9d3cd8_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp 1.4.0 h2c329e2_0 conda-forge
libwebp-base 1.4.0 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.7.0 h662e7e4_0 conda-forge
libxml2 2.12.7 h4c95cb1_3 conda-forge
libxslt 1.1.39 h76b75d6_0 conda-forge
libzip 1.11.2 h6991a6a_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
linopy 0.3.14 pyhd8ed1ab_0 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
logmuse 0.2.8 pyhd8ed1ab_1 conda-forge
lxml 4.9.3 py311h1a07684_3 conda-forge
lz4 4.3.3 py311h2cbdf9a_1 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 hd590300_1001 conda-forge
mapclassify 2.8.1 pyhd8ed1ab_1 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_1 conda-forge
markupsafe 3.0.2 py311h2dc5d0c_1 conda-forge
matplotlib 3.8.0 py311h38be061_2 conda-forge
matplotlib-base 3.8.0 py311h54ef318_2 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_1 conda-forge
mccabe 0.7.0 pypi_0 pypi
mdurl 0.1.2 pyhd8ed1ab_1 conda-forge
memory_profiler 0.61.0 pyhd8ed1ab_1 conda-forge
metis 5.1.0 hd0bcaf9_1007 conda-forge
minizip 4.0.9 h05a5f5f_0 conda-forge
mistune 3.1.3 pyh29332c3_0 conda-forge
mpg123 1.32.9 hc50e24c_0 conda-forge
msgpack-python 1.1.0 py311hd18a35c_0 conda-forge
multidict 6.3.2 py311h2dc5d0c_0 conda-forge
multiurl 0.3.5 pyhd8ed1ab_0 conda-forge
mumps-include 5.7.3 h23d43cc_9 conda-forge
mumps-seq 5.7.3 h27a6a8b_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.33 hf1915f5_6 conda-forge
mysql-libs 8.0.33 hca2cd23_6 conda-forge
narwhals 1.34.0 pyhd8ed1ab_0 conda-forge
nbclient 0.10.2 pyhd8ed1ab_0 conda-forge
nbconvert 7.16.6 hb482800_0 conda-forge
nbconvert-core 7.16.6 pyh29332c3_0 conda-forge
nbconvert-pandoc 7.16.6 hed9df3c_0 conda-forge
nbformat 5.10.4 pyhd8ed1ab_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_1 conda-forge
netcdf4 1.6.4 nompi_py311he8ad708_103 conda-forge
networkx 3.1 pyhd8ed1ab_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
notebook 7.0.6 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.4 pyhd8ed1ab_1 conda-forge
nspr 4.36 h5888daf_0 conda-forge
nss 3.110 h159eef7_0 conda-forge
numexpr 2.10.2 py311h38b10cd_100 conda-forge
numpy 1.26.0 py311h64a7726_0 conda-forge
oauth2client 4.1.3 pyhd8ed1ab_1 conda-forge
openjdk 22.0.1 hb622114_0 conda-forge
openjpeg 2.5.2 h488ebb8_0 conda-forge
openpyxl 3.1.2 py311h459d7ec_1 conda-forge
openssl 3.4.1 h7b32b05_0 conda-forge
orc 2.0.3 he039a57_0 conda-forge
overrides 7.7.0 pyhd8ed1ab_1 conda-forge
packaging 24.2 pyhd8ed1ab_2 conda-forge
pandas 2.2.2 py311h14de704_1 conda-forge
pandoc 3.6.4 ha770c72_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
pango 1.52.1 ha41ecd1_0 conda-forge
paramiko 3.5.1 pyhd8ed1ab_0 conda-forge
parso 0.8.4 pyhd8ed1ab_1 conda-forge
partd 1.4.2 pyhd8ed1ab_0 conda-forge
patsy 1.0.1 pyhd8ed1ab_1 conda-forge
pcre2 10.42 hcad00b1_0 conda-forge
pephubclient 0.4.4 pyhd8ed1ab_1 conda-forge
peppy 0.40.7 pyhd8ed1ab_2 conda-forge
pexpect 4.9.0 pyhd8ed1ab_1 conda-forge
pickleshare 0.7.5 pyhd8ed1ab_1004 conda-forge
pillow 10.3.0 py311h18e6fac_0 conda-forge
pip 25.0.1 pyh8b19718_0 conda-forge
pixman 0.44.2 h29eaf8c_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_2 conda-forge
plac 1.4.5 pyhd8ed1ab_0 conda-forge
platformdirs 4.3.7 pyh29332c3_0 conda-forge
plotly 5.17.0 pyhd8ed1ab_0 conda-forge
pluggy 1.5.0 pyhd8ed1ab_1 conda-forge
ply 3.11 pyhd8ed1ab_3 conda-forge
polars 1.26.0 py311h03f6b34_0 conda-forge
poppler 23.12.0 h590f24d_0 conda-forge
poppler-data 0.4.12 hd8ed1ab_0 conda-forge
postgresql 16.4 hb2eb5c0_3 conda-forge
prettytable 3.16.0 pyhd8ed1ab_0 conda-forge
progressbar2 4.3.2 pyhd8ed1ab_0 conda-forge
proj 9.3.0 h1d62c97_2 conda-forge
prometheus_client 0.21.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.50 pyha770c72_0 conda-forge
prompt_toolkit 3.0.50 hd8ed1ab_0 conda-forge
propcache 0.2.1 py311h2dc5d0c_1 conda-forge
proto-plus 1.26.1 pyhd8ed1ab_0 conda-forge
protobuf 5.28.2 py311hfdbb021_0 conda-forge
psutil 7.0.0 py311h9ecbd09_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
ptyprocess 0.7.0 pyhd8ed1ab_1 conda-forge
pulp 2.7.0 py311h38be061_1 conda-forge
pulseaudio-client 16.1 hb77b528_5 conda-forge
pure_eval 0.2.3 pyhd8ed1ab_1 conda-forge
py-cpuinfo 9.0.0 pyhd8ed1ab_1 conda-forge
pyarrow 16.1.0 py311hbd00459_6 conda-forge
pyarrow-core 16.1.0 py311h4854187_6_cpu conda-forge
pyasn1 0.6.1 pyhd8ed1ab_2 conda-forge
pyasn1-modules 0.4.2 pyhd8ed1ab_0 conda-forge
pycodestyle 2.13.0 pypi_0 pypi
pycountry 22.3.5 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pydantic 2.11.2 pyh3cfb1c2_0 conda-forge
pydantic-core 2.33.1 py311h687327b_0 conda-forge
pyflakes 3.3.2 pypi_0 pypi
pygments 2.19.1 pyhd8ed1ab_0 conda-forge
pynacl 1.5.0 py311h9ecbd09_4 conda-forge
pyogrio 0.7.2 py311hbac4ec9_0 conda-forge
pyomo 6.6.1 py311hb755f60_0 conda-forge
pyopenssl 25.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.2.3 pyhd8ed1ab_1 conda-forge
pyproj 3.6.1 py311h1facc83_4 conda-forge
pypsa 0.30.2 pyhd8ed1ab_1 conda-forge
pyqt 5.15.9 py311hf0fb5b6_5 conda-forge
pyqt5-sip 12.12.2 py311hb755f60_5 conda-forge
pysftp 0.2.9 py_1 conda-forge
pyshp 2.3.1 pyhd8ed1ab_1 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
pytables 3.9.1 py311h10c7f7f_0 conda-forge
pytest 8.3.5 pyhd8ed1ab_0 conda-forge
python 3.11.9 hb806964_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhff2d567_1 conda-forge
python-fastjsonschema 2.21.1 pyhd8ed1ab_0 conda-forge
python-irodsclient 2.1.0 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python-utils 3.9.1 pyhff2d567_1 conda-forge
python_abi 3.11 6_cp311 conda-forge
pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_1 conda-forge
pyyaml 6.0.2 py311h2dc5d0c_2 conda-forge
pyzmq 26.4.0 py311h7deb3e3_0 conda-forge
qt-main 5.15.8 h5810be5_19 conda-forge
qtconsole-base 5.6.1 pyha770c72_1 conda-forge
qtpy 2.4.3 pyhd8ed1ab_0 conda-forge
rasterio 1.3.8 py311h40fbdff_4 conda-forge
re2 2024.07.02 h9925aae_2 conda-forge
readline 8.2 h8c095d6_2 conda-forge
referencing 0.36.2 pyh29332c3_0 conda-forge
requests 2.32.3 pyhd8ed1ab_1 conda-forge
reretry 0.11.8 pyhd8ed1ab_1 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_1 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rich 14.0.0 pyh29332c3_0 conda-forge
rpds-py 0.24.0 py311h687327b_0 conda-forge
rsa 4.9 pyhd8ed1ab_1 conda-forge
s2n 1.5.9 h0fd0ee4_0 conda-forge
s3transfer 0.11.4 pyhd8ed1ab_0 conda-forge
scikit-learn 1.6.1 py311h57cc02b_0 conda-forge
scipy 1.11.3 py311h64a7726_1 conda-forge
seaborn 0.13.2 hd8ed1ab_3 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_3 conda-forge
send2trash 1.8.3 pyh0d859eb_1 conda-forge
setuptools 78.1.0 pyhff2d567_0 conda-forge
setuptools-scm 8.2.1 pyhd8ed1ab_0 conda-forge
setuptools_scm 8.2.1 hd8ed1ab_0 conda-forge
shapely 2.0.2 py311h2032efe_1 conda-forge
shellingham 1.5.4 pyhd8ed1ab_1 conda-forge
sip 6.7.12 py311hb755f60_0 conda-forge
six 1.17.0 pyhd8ed1ab_0 conda-forge
slacker 0.14.0 pyhd8ed1ab_1 conda-forge
smart_open 7.1.0 pyhd8ed1ab_0 conda-forge
smmap 5.0.2 pyhd8ed1ab_0 conda-forge
snakemake 7.32.4 hdfd78af_1 bioconda
snakemake-minimal 7.32.4 pyhdfd78af_1 bioconda
snappy 1.2.1 h8bd8927_1 conda-forge
sniffio 1.3.1 pyhd8ed1ab_1 conda-forge
snuggs 1.4.7 pyhd8ed1ab_2 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_1 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
sqlite 3.49.1 h9eae976_2 conda-forge
stack_data 0.6.3 pyhd8ed1ab_1 conda-forge
statsmodels 0.14.4 py311h9f3472d_0 conda-forge
stone 3.3.2 pyhd8ed1ab_0 conda-forge
stopit 1.1.2 pyhd8ed1ab_1 conda-forge
tabula-py 2.7.0 py311h38be061_1 conda-forge
tabulate 0.9.0 pyhd8ed1ab_2 conda-forge
tblib 3.1.0 pyhd8ed1ab_0 conda-forge
tenacity 9.1.2 pyhd8ed1ab_0 conda-forge
terminado 0.18.1 pyh0d859eb_0 conda-forge
threadpoolctl 3.6.0 pyhecae5ae_0 conda-forge
throttler 1.2.2 pyhd8ed1ab_0 conda-forge
tiledb 2.18.2 h99f50a1_1 conda-forge
tinycss2 1.4.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_1 conda-forge
tomli 2.2.1 pyhd8ed1ab_1 conda-forge
toolz 1.0.0 pyhd8ed1ab_1 conda-forge
toposort 1.10 pyhd8ed1ab_1 conda-forge
tornado 6.4.2 py311h9ecbd09_0 conda-forge
tqdm 4.66.1 pyhd8ed1ab_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
tsam 2.3.6 pypi_0 pypi
typer 0.15.2 pyhff008b6_0 conda-forge
typer-slim 0.15.2 pyh29332c3_0 conda-forge
typer-slim-standard 0.15.2 h801b22e_0 conda-forge
types-python-dateutil 2.9.0.20241206 pyhd8ed1ab_0 conda-forge
typing-extensions 4.13.1 hf5ce1d7_0 conda-forge
typing-inspection 0.4.0 pyhd8ed1ab_0 conda-forge
typing_extensions 4.13.1 pyh29332c3_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge
tzcode 2025b hb9d3cd8_0 conda-forge
tzdata 2025b h78e105d_0 conda-forge
ubiquerg 0.8.0 pyhd8ed1ab_0 conda-forge
unicodedata2 16.0.0 py311h9ecbd09_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
uriparser 0.9.8 hac33072_0 conda-forge
uritemplate 4.1.1 pyhd8ed1ab_1 conda-forge
urllib3 2.3.0 pyhd8ed1ab_0 conda-forge
validators 0.34.0 pyhd8ed1ab_1 conda-forge
veracitools 0.1.3 py_0 conda-forge
vresutils 0.3.1 pypi_0 pypi
wcwidth 0.2.13 pyhd8ed1ab_1 conda-forge
webcolors 24.11.1 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_1 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.13 pyhd8ed1ab_1 conda-forge
wrapt 1.17.2 py311h9ecbd09_0 conda-forge
xarray 2024.9.0 pyhd8ed1ab_1 conda-forge
xcb-util 0.4.0 hd590300_1 conda-forge
xcb-util-image 0.4.0 h8ee46fc_1 conda-forge
xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge
xcb-util-renderutil 0.3.9 hd590300_1 conda-forge
xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge
xerces-c 3.2.5 hac6953d_0 conda-forge
xkeyboard-config 2.42 h4ab18f5_0 conda-forge
xlrd 2.0.1 pyhd8ed1ab_3 conda-forge
xorg-fixesproto 5.0 hb9d3cd8_1003 conda-forge
xorg-inputproto 2.3.2 hb9d3cd8_1003 conda-forge
xorg-kbproto 1.0.7 hb9d3cd8_1003 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.9 h8ee46fc_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h4bc722e_1 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-libxtst 1.2.5 h4bc722e_0 conda-forge
xorg-recordproto 1.14.2 hb9d3cd8_1003 conda-forge
xorg-renderproto 0.11.1 hb9d3cd8_1003 conda-forge
xorg-xextproto 7.3.0 hb9d3cd8_1004 conda-forge
xorg-xf86vidmodeproto 2.3.1 hb9d3cd8_1005 conda-forge
xorg-xproto 7.0.31 hb9d3cd8_1008 conda-forge
xyzservices 2025.1.0 pyhd8ed1ab_0 conda-forge
xz 5.8.1 hbcc6ac9_0 conda-forge
xz-gpl-tools 5.8.1 hbcc6ac9_0 conda-forge
xz-tools 5.8.1 hb9d3cd8_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.18.3 py311h2dc5d0c_1 conda-forge
yte 1.7.0 pyha770c72_1 conda-forge
zeromq 4.3.5 h3b0a872_7 conda-forge
zict 3.0.0 pyhd8ed1ab_1 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
zstandard 0.23.0 py311h9ecbd09_1 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge
Anything else?
No response
Thank you for raising the issue, @jaclynr109! And sorry you are experiencing so many environment issues.
Just to confirm, you only get this error when you run on the HPC? Or do you experience this issue if running locally as well? Also, if you do a dry run (ie. add the -n flag to the snakemake call), do you still get the issue?
Unfortunately, I probably wont be too helpful troubleshooting conda on the HPC. The HPC I run on doesn't allow conda installations. Rather, I just use their (the HPC's) pre-installed modules for the big packages (ie. scikitlearn, gurobi, ect..) and installed any remaining packages via pip into an venv. That seemed to work for me, but is a little tedious to get setup.
