From f678adfddc2ed314ec8d72351b90d344d946e955 Mon Sep 17 00:00:00 2001
From: _ <4256466+leehart@users.noreply.github.com>
Date: Thu, 14 Nov 2024 11:08:55 -0600
Subject: [PATCH 1/8] Ignore .ipynb_checkpoints

---
 .gitignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitignore b/.gitignore
index 9bcfa57..c587a77 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,5 @@ deps
 export
 # pycharm
 .idea
+# Jupyter
+.ipynb_checkpoints

From 034b1924ed6ebea6ff0f8d8aa9cb1450d52348c6 Mon Sep 17 00:00:00 2001
From: _ <4256466+leehart@users.noreply.github.com>
Date: Thu, 14 Nov 2024 11:11:15 -0600
Subject: [PATCH 2/8] WIP: diagnostic: remove failing code

---
 install-conda.sh | 24 ++----------------------
 1 file changed, 2 insertions(+), 22 deletions(-)

diff --git a/install-conda.sh b/install-conda.sh
index 6dfbad9..77f32e5 100755
--- a/install-conda.sh
+++ b/install-conda.sh
@@ -79,29 +79,9 @@ fi
 ENVPINNED=${MGENVDIR}/environment-pinned-${OS}.yml
 
 if [ -f "$ENVPINNED" ]; then
-    # Here we build the environment from the pinned definition file,
-    # this is what we expect users to do.
-    echo "[mgenv] creating environment $CONDANAME from $ENVPINNED"
-    conda env create -v --yes --name $CONDANAME --file $ENVPINNED
+    echo "got pinned"
 
 else
-    # Here we rebuild the environment from the unpinned requirements files,
-    # which is what a maintainer will do when they want to upgrade the pinned
-    # definition files.
-    conda env remove -v --name=$CONDANAME
-    echo "[mgenv] recreating $ENVPINNED"
-    echo "[mgenv] installing conda packages"
-    conda create --yes -v --strict-channel-priority $CHANNEL_OPTS --name $CONDANAME --file ${MGENVDIR}/requirements-conda.txt --file ${MGENVDIR}/requirements-compilers-${OS}.txt
-    echo "[mgenv] installing packages from pypi"
-    source activate $CONDANAME
-    pip install -v -r ${MGENVDIR}/requirements-pypi.txt
-    echo "[mgenv] exporting environment"
-    # N.B., here we add the conda-forge/label/broken channel so that the install
-    # will still work in the future, even if some conda-forge packages have been
-    # moved to the broken channel.
-    conda env export -v $CHANNEL_OPTS --channel=conda-forge/label/broken --name=$CONDANAME > $ENVPINNED
-    echo "*** $ENVPINNED ***"
-    cat $ENVPINNED
-    echo "*** $ENVPINNED ***"
+    echo "not got pinned"
 
 fi

From 9ce4cf7bca728f017a514819633dfb04b014b0a0 Mon Sep 17 00:00:00 2001
From: _ <4256466+leehart@users.noreply.github.com>
Date: Thu, 14 Nov 2024 11:13:53 -0600
Subject: [PATCH 3/8] Remove pinned env files

---
 environment-pinned-macos-latest.yml  | 739 -------------------------
 environment-pinned-ubuntu-latest.yml | 780 ---------------------------
 2 files changed, 1519 deletions(-)
 delete mode 100644 environment-pinned-macos-latest.yml
 delete mode 100644 environment-pinned-ubuntu-latest.yml

diff --git a/environment-pinned-macos-latest.yml b/environment-pinned-macos-latest.yml
deleted file mode 100644
index 29f7bd2..0000000
--- a/environment-pinned-macos-latest.yml
+++ /dev/null
@@ -1,739 +0,0 @@
-name: mgenv-24fa320
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-  - conda-forge/label/broken
-dependencies:
-  - accessible-pygments=0.0.5=pyhd8ed1ab_0
-  - adal=1.2.7=pyhd8ed1ab_0
-  - adlfs=2024.7.0=pyhd8ed1ab_0
-  - affine=2.4.0=pyhd8ed1ab_0
-  - aiobotocore=2.15.1=pyhd8ed1ab_0
-  - aiohappyeyeballs=2.4.0=pyhd8ed1ab_0
-  - aiohttp=3.10.5=py312hb553811_1
-  - aioitertools=0.12.0=pyhd8ed1ab_0
-  - aiosignal=1.3.1=pyhd8ed1ab_0
-  - alabaster=0.7.16=pyhd8ed1ab_0
-  - altair=5.4.1=pyhd8ed1ab_0
-  - amply=0.1.6=pyhd8ed1ab_0
-  - anyio=4.6.0=pyhd8ed1ab_1
-  - aom=3.9.1=hf036a51_0
-  - appdirs=1.4.4=pyh9f0ad1d_0
-  - appnope=0.1.4=pyhd8ed1ab_0
-  - apricot-select=0.6.1=pyhd8ed1ab_0
-  - argon2-cffi=23.1.0=pyhd8ed1ab_0
-  - argon2-cffi-bindings=21.2.0=py312hb553811_5
-  - argparse-dataclass=2.0.0=pyhd8ed1ab_0
-  - arrow=1.3.0=pyhd8ed1ab_0
-  - asciitree=0.3.3=py_2
-  - asteval=1.0.4=pyhd8ed1ab_0
-  - asttokens=2.4.1=pyhd8ed1ab_0
-  - atk-1.0=2.38.0=h4bec284_2
-  - attmap=0.13.2=pyhd8ed1ab_0
-  - attrs=24.2.0=pyh71513ae_0
-  - aws-c-auth=0.7.31=hb28a666_0
-  - aws-c-cal=0.7.4=h8128ea2_1
-  - aws-c-common=0.9.28=h00291cd_0
-  - aws-c-compression=0.2.19=h8128ea2_1
-  - aws-c-event-stream=0.4.3=hcd1ed9e_2
-  - aws-c-http=0.8.10=h2f86973_0
-  - aws-c-io=0.14.18=hf9a0f1c_10
-  - aws-c-mqtt=0.10.6=h9d7d61c_0
-  - aws-c-s3=0.6.6=hd01826e_0
-  - aws-c-sdkutils=0.1.19=h8128ea2_3
-  - aws-checksums=0.1.20=h8128ea2_0
-  - aws-crt-cpp=0.28.3=h21c617a_5
-  - aws-sdk-cpp=1.11.407=h2e282c2_0
-  - azure-core=1.31.0=pyhd8ed1ab_0
-  - azure-core-cpp=1.13.0=hf8dbe3c_0
-  - azure-datalake-store=0.0.51=pyh9f0ad1d_0
-  - azure-identity=1.17.1=pyhd8ed1ab_0
-  - azure-identity-cpp=1.8.0=h60298e3_2
-  - azure-storage-blob=12.23.0=pyhd8ed1ab_0
-  - azure-storage-blobs-cpp=12.12.0=h646f05d_0
-  - azure-storage-common-cpp=12.7.0=hf91904f_1
-  - azure-storage-files-datalake-cpp=12.11.0=h14965f0_1
-  - babel=2.14.0=pyhd8ed1ab_0
-  - backoff=2.2.1=pyhd8ed1ab_0
-  - bcftools=1.21=h0126a07_0
-  - bcrypt=4.2.0=py312h669792a_1
-  - beautifulsoup4=4.12.3=pyha770c72_0
-  - biopython=1.84=py312hbd25219_0
-  - black=24.8.0=py312hb401068_1
-  - blas=2.122=openblas
-  - blas-devel=3.9.0=22_osx64_openblas
-  - bleach=6.1.0=pyhd8ed1ab_0
-  - blinker=1.8.2=pyhd8ed1ab_0
-  - blosc=1.21.6=h7d75f6d_0
-  - bokeh=3.5.2=pyhd8ed1ab_0
-  - boto3=1.35.23=pyhd8ed1ab_0
-  - botocore=1.35.23=pyge310_1234567_0
-  - bqplot=0.12.43=pyhd8ed1ab_0
-  - branca=0.7.2=pyhd8ed1ab_0
-  - brotli=1.1.0=h00291cd_2
-  - brotli-bin=1.1.0=h00291cd_2
-  - brotli-python=1.1.0=py312h5861a67_2
-  - brunsli=0.1=h046ec9c_0
-  - bzip2=1.0.8=hfdf4475_7
-  - c-ares=1.33.1=h44e7173_0
-  - c-blosc2=2.15.1=hb9356d3_0
-  - ca-certificates=2024.8.30=h8857fd0_0
-  - cached-property=1.5.2=hd8ed1ab_1
-  - cached_property=1.5.2=pyha770c72_1
-  - cachetools=5.5.0=pyhd8ed1ab_0
-  - cairo=1.18.0=h37bd5c4_3
-  - cartopy=0.23.0=py312h98e817e_2
-  - cctools_osx-64=1010.6=h525afad_1
-  - certifi=2024.8.30=pyhd8ed1ab_0
-  - cffi=1.17.1=py312hf857d28_0
-  - cfitsio=4.4.1=ha105788_0
-  - cftime=1.6.4=py312h3a11e2b_1
-  - charls=2.4.2=he965462_0
-  - charset-normalizer=3.3.2=pyhd8ed1ab_0
-  - clang=18.1.8=default_h179603d_5
-  - clang-18=18.1.8=default_h0c94c6a_5
-  - clang_impl_osx-64=18.1.8=h6a44ed1_19
-  - clang_osx-64=18.1.8=hb91bd55_19
-  - clangxx=18.1.8=default_h179603d_5
-  - clangxx_impl_osx-64=18.1.8=h4b7810f_19
-  - clangxx_osx-64=18.1.8=hb91bd55_19
-  - click=8.1.7=unix_pyh707e725_0
-  - click-plugins=1.1.1=py_0
-  - cligj=0.7.2=pyhd8ed1ab_1
-  - cloudpickle=3.0.0=pyhd8ed1ab_0
-  - coiled=1.50.0=pyhd8ed1ab_0
-  - coin-or-cbc=2.10.12=h26cd4a2_1
-  - coin-or-cgl=0.60.9=h5c63661_0
-  - coin-or-clp=1.17.10=hf05e7e8_0
-  - coin-or-osi=0.108.11=h8c189bd_1
-  - coin-or-utils=2.11.12=h95c8798_1
-  - coincbc=2.10.12=1_metapackage
-  - colorama=0.4.6=pyhd8ed1ab_0
-  - colorcet=3.1.0=pyhd8ed1ab_0
-  - comm=0.2.2=pyhd8ed1ab_0
-  - compiler-rt=18.1.8=h1020d70_1
-  - compiler-rt_osx-64=18.1.8=hf2b8a54_1
-  - conda-inject=1.3.2=pyhd8ed1ab_0
-  - configargparse=1.7=pyhd8ed1ab_0
-  - connection_pool=0.0.3=pyhd3deb0d_0
-  - contourpy=1.3.0=py312hc5c4d5f_1
-  - coverage=7.6.1=py312hb553811_1
-  - cramjam=2.8.4rc3=py312h45123d6_2
-  - cryptography=43.0.1=py312h840e0bc_0
-  - cycler=0.12.1=pyhd8ed1ab_0
-  - cython=3.0.11=py312h5861a67_2
-  - cytoolz=0.12.3=py312h41838bb_0
-  - dash=2.18.1=pyhd8ed1ab_0
-  - dask=2024.9.0=pyhd8ed1ab_0
-  - dask-core=2024.9.0=pyhd8ed1ab_0
-  - dask-expr=1.1.14=pyhd8ed1ab_0
-  - dask-gateway=2022.10.0=pyh8af1aa0_0
-  - dask-glm=0.3.2=pyhd8ed1ab_0
-  - dask-ml=2024.4.4=pyhd8ed1ab_0
-  - datashader=0.16.3=pyhd8ed1ab_0
-  - datrie=0.8.2=py312hb553811_8
-  - dav1d=1.2.1=h0dc2134_0
-  - debugpy=1.8.5=py312h5861a67_1
-  - decorator=5.1.1=pyhd8ed1ab_0
-  - defusedxml=0.7.1=pyhd8ed1ab_0
-  - demes=0.2.3=pyhd8ed1ab_0
-  - deprecated=1.2.14=pyh1a96a4e_0
-  - dill=0.3.8=pyhd8ed1ab_0
-  - distributed=2024.9.0=pyhd8ed1ab_0
-  - docutils=0.20.1=py312hb401068_3
-  - dpath=2.2.0=pyha770c72_0
-  - eido=0.2.2=pyhd8ed1ab_0
-  - entrypoints=0.4=pyhd8ed1ab_0
-  - et_xmlfile=1.1.0=pyhd8ed1ab_0
-  - exceptiongroup=1.2.2=pyhd8ed1ab_0
-  - executing=2.1.0=pyhd8ed1ab_0
-  - expat=2.6.3=hac325c4_0
-  - fabric=3.2.2=pyhd8ed1ab_0
-  - fastcluster=1.2.6=py312h81f2e74_4
-  - fasteners=0.17.3=pyhd8ed1ab_0
-  - fastparquet=2024.5.0=py312h5dc8b90_0
-  - filelock=3.16.1=pyhd8ed1ab_0
-  - flake8=7.1.1=pyhd8ed1ab_0
-  - flask=3.0.3=pyhd8ed1ab_0
-  - fmt=11.0.2=h3c5361c_0
-  - folium=0.17.0=pyhd8ed1ab_0
-  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
-  - font-ttf-inconsolata=3.000=h77eed37_0
-  - font-ttf-source-code-pro=2.038=h77eed37_0
-  - font-ttf-ubuntu=0.83=h77eed37_2
-  - fontconfig=2.14.2=h5bb23bf_0
-  - fonts-conda-ecosystem=1=0
-  - fonts-conda-forge=1=0
-  - fonttools=4.54.0=py312hb553811_0
-  - fqdn=1.5.1=pyhd8ed1ab_0
-  - freetype=2.12.1=h60636b9_2
-  - freexl=2.0.0=h3ec172f_0
-  - fribidi=1.0.10=hbcb3906_0
-  - frozenlist=1.4.1=py312hb553811_1
-  - fsspec=2024.9.0=pyhff2d567_0
-  - fusepy=3.0.1=py_0
-  - future=1.0.0=pyhd8ed1ab_0
-  - gast=0.4.0=pyh9f0ad1d_0
-  - gcsfs=2024.9.0=pyhd8ed1ab_0
-  - gdal=3.9.2=py312h365dfcf_4
-  - gdk-pixbuf=2.42.12=ha587570_0
-  - geopandas=1.0.1=pyhd8ed1ab_1
-  - geopandas-base=1.0.1=pyha770c72_1
-  - geos=3.12.2=hf036a51_1
-  - geotiff=1.7.3=h2b6e260_3
-  - geoviews=1.13.0=hd8ed1ab_0
-  - geoviews-core=1.13.0=pyha770c72_0
-  - gettext=0.22.5=hdfe23c8_3
-  - gettext-tools=0.22.5=hdfe23c8_3
-  - gflags=2.2.2=hac325c4_1005
-  - gfortran_impl_osx-64=13.2.0=h2bc304d_3
-  - gfortran_osx-64=13.2.0=h18f7dce_1
-  - giflib=5.2.2=h10d778d_0
-  - gilknocker=0.4.1=py312h669792a_4
-  - gitdb=4.0.11=pyhd8ed1ab_0
-  - gitpython=3.1.43=pyhd8ed1ab_0
-  - glog=0.7.1=h2790a97_0
-  - gmp=6.3.0=hf036a51_2
-  - gmpy2=2.1.5=py312h165121d_2
-  - google-api-core=2.19.2=pyhd8ed1ab_0
-  - google-auth=2.35.0=pyhff2d567_0
-  - google-auth-oauthlib=1.2.1=pyhd8ed1ab_0
-  - google-cloud-core=2.4.1=pyhd8ed1ab_0
-  - google-cloud-sdk=493.0.0=py312hb401068_0
-  - google-cloud-storage=2.18.2=pyhff2d567_0
-  - google-crc32c=1.1.2=py312hfee8fbb_6
-  - google-resumable-media=2.7.2=pyhd8ed1ab_1
-  - googleapis-common-protos=1.65.0=pyhd8ed1ab_0
-  - graphite2=1.3.13=h73e2aa4_1003
-  - graphviz=12.0.0=he14ced1_0
-  - greenlet=3.1.1=py312h5861a67_0
-  - grpcio=1.62.2=py312hbbbd34f_0
-  - gsl=2.7=h93259b0_0
-  - gtk2=2.24.33=h2c15c3c_5
-  - gts=0.7.6=h53e17e3_4
-  - h11=0.14.0=pyhd8ed1ab_0
-  - h2=4.1.0=pyhd8ed1ab_0
-  - h5py=3.11.0=nompi_py312hfc94b03_102
-  - harfbuzz=9.0.0=h098a298_1
-  - hdf4=4.2.15=h8138101_7
-  - hdf5=1.14.3=nompi_h687a608_105
-  - hmmlearn=0.3.2=py312h5861a67_1
-  - holoviews=1.19.1=pyhd8ed1ab_0
-  - hpack=4.0.0=pyh9f0ad1d_0
-  - htslib=1.21=hec81eee_0
-  - httpcore=1.0.5=pyhd8ed1ab_0
-  - httpx=0.27.2=pyhd8ed1ab_0
-  - humanfriendly=10.0=pyhd8ed1ab_6
-  - humanize=4.10.0=pyhd8ed1ab_0
-  - hvplot=0.10.0=pyhd8ed1ab_0
-  - hyperframe=6.0.1=pyhd8ed1ab_0
-  - icu=75.1=h120a0e1_0
-  - idna=3.10=pyhd8ed1ab_0
-  - imagecodecs=2024.6.1=py312h2bbe148_4
-  - imageio=2.35.1=pyh12aca89_0
-  - imagesize=1.4.1=pyhd8ed1ab_0
-  - immutables=0.20=py312h104f124_1
-  - importlib-metadata=7.2.1=pyha770c72_0
-  - importlib_metadata=7.2.1=hd8ed1ab_0
-  - importlib_resources=6.4.5=pyhd8ed1ab_0
-  - importnb=2023.11.1=pyhd8ed1ab_0
-  - iniconfig=2.0.0=pyhd8ed1ab_0
-  - intake=2.0.7=pyhd8ed1ab_0
-  - intake-xarray=0.7.0=pyhd8ed1ab_0
-  - intervaltree=3.1.0=pyhd8ed1ab_1
-  - invoke=2.2.0=pyhd8ed1ab_0
-  - ipydatagrid=1.3.2=pyhd8ed1ab_0
-  - ipyigv=0.1.9=pyhe74cb21_0
-  - ipykernel=6.29.5=pyh57ce528_0
-  - ipyleaflet=0.19.2=pyhd8ed1ab_0
-  - ipympl=0.9.4=pyhd8ed1ab_0
-  - ipython=8.27.0=pyh707e725_0
-  - ipython_genutils=0.2.0=pyhd8ed1ab_1
-  - ipytree=0.2.2=pyhd8ed1ab_0
-  - ipywidgets=7.6.5=pyhd8ed1ab_0
-  - isl=0.26=imath32_h2e86a7b_101
-  - iso3166=2.1.1=pyhd8ed1ab_0
-  - isodate=0.6.1=pyhd8ed1ab_0
-  - isoduration=20.11.0=pyhd8ed1ab_0
-  - isort=5.13.2=pyhd8ed1ab_0
-  - itsdangerous=2.2.0=pyhd8ed1ab_0
-  - jedi=0.19.1=pyhd8ed1ab_0
-  - jinja2=3.1.4=pyhd8ed1ab_0
-  - jmespath=1.0.1=pyhd8ed1ab_0
-  - joblib=1.4.2=pyhd8ed1ab_0
-  - json-c=0.18=hc62ec3d_0
-  - json5=0.9.25=pyhd8ed1ab_0
-  - jsondiff=2.0.0=pyhd8ed1ab_0
-  - jsonpointer=3.0.0=py312hb401068_1
-  - jsonschema=4.23.0=pyhd8ed1ab_0
-  - jsonschema-specifications=2023.12.1=pyhd8ed1ab_0
-  - jsonschema-with-format-nongpl=4.23.0=hd8ed1ab_0
-  - jupyter=1.1.1=pyhd8ed1ab_0
-  - jupyter-book=1.0.2=pyhd8ed1ab_0
-  - jupyter-cache=1.0.0=pyhd8ed1ab_0
-  - jupyter-resource-usage=0.7.1=pyhd8ed1ab_0
-  - jupyter_client=7.4.9=pyhd8ed1ab_0
-  - jupyter_console=6.6.3=pyhd8ed1ab_0
-  - jupyter_core=5.7.2=pyh31011fe_1
-  - jupyter_events=0.10.0=pyhd8ed1ab_0
-  - jupyter_leaflet=0.19.2=pyhd8ed1ab_0
-  - jupyter_server=2.14.2=pyhd8ed1ab_0
-  - jupyter_server_terminals=0.5.3=pyhd8ed1ab_0
-  - jupyterlab=3.5.3=pyhd8ed1ab_0
-  - jupyterlab-system-monitor=0.8.0=pyhd8ed1ab_2
-  - jupyterlab-topbar=0.6.1=pyhd8ed1ab_2
-  - jupyterlab-variableinspector=3.2.4=pyhd8ed1ab_0
-  - jupyterlab_code_formatter=3.0.2=pyhd8ed1ab_0
-  - jupyterlab_launcher=0.13.1=py_2
-  - jupyterlab_pygments=0.3.0=pyhd8ed1ab_0
-  - jupyterlab_server=2.27.3=pyhd8ed1ab_0
-  - jupyterlab_widgets=3.0.13=pyhd8ed1ab_0
-  - jupytext=1.16.4=pyh80e38bb_0
-  - jxrlib=1.1=h10d778d_3
-  - kealib=1.5.3=he475af8_2
-  - kiwisolver=1.4.7=py312hc5c4d5f_0
-  - krb5=1.21.3=h37d8d59_0
-  - latexcodec=2.0.1=pyh9f0ad1d_0
-  - lazy-loader=0.4=pyhd8ed1ab_1
-  - lazy_loader=0.4=pyhd8ed1ab_1
-  - lcms2=2.16=ha2f27b4_0
-  - ld64_osx-64=951.9=h4c85b5e_1
-  - lerc=4.0.0=hb486fe8_0
-  - libabseil=20240116.2=cxx17_hf036a51_1
-  - libaec=1.1.3=h73e2aa4_0
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-  - xerces-c=3.2.5=hfb503d4_1
-  - xlrd=2.0.1=pyhd8ed1ab_3
-  - xlwt=1.3.0=py_1
-  - xorg-libxau=1.0.11=h00291cd_1
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-  - yarl=1.9.4=py312hb553811_1
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-  - zstd=1.5.6=h915ae27_0
-  - pip:
-      - biotite==1.0.1
-      - biotraj==1.2.1
-      - dash-core-components==2.0.0
-      - dash-cytoscape==1.0.2
-      - dash-html-components==2.0.0
-      - dash-table==5.0.0
-      - igv-notebook==0.5.2
-      - ipinfo==5.1.1
-      - lxml==5.3.0
-      - lxml-html-clean==0.2.2
-      - malariagen-data==13.2.1
-      - numpydoc-decorator==2.2.1
-      - orjson==3.10.7
-      - petlx==1.0.3
-      - protopunica==0.14.8.post2
-      - pyerf==1.0.1
-      - pyfaidx==0.8.1.2
-      - python-gist==0.10.6
-      - python-gnupg==0.4.9
-      - scikit-allel==1.3.13
-      - scikits-bootstrap==1.1.0
-      - sgkit==0.9.0
-      - sh==2.0.7
-      - termcolor==2.3.0
-      - typeguard==4.3.0
-      - yaspin==3.1.0
-prefix: /Users/runner/work/mgenv/mgenv/deps/conda/envs/mgenv-24fa320
diff --git a/environment-pinned-ubuntu-latest.yml b/environment-pinned-ubuntu-latest.yml
deleted file mode 100644
index fef1cd7..0000000
--- a/environment-pinned-ubuntu-latest.yml
+++ /dev/null
@@ -1,780 +0,0 @@
-name: mgenv-24fa320
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-  - conda-forge/label/broken
-dependencies:
-  - _libgcc_mutex=0.1=conda_forge
-  - _openmp_mutex=4.5=2_kmp_llvm
-  - _sysroot_linux-64_curr_repodata_hack=3=h69a702a_16
-  - accessible-pygments=0.0.5=pyhd8ed1ab_0
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-  - aws-c-auth=0.7.31=h57bd9a3_0
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-  - aws-c-compression=0.2.19=h756ea98_1
-  - aws-c-event-stream=0.4.3=h29ce20c_2
-  - aws-c-http=0.8.10=h5e77a74_0
-  - aws-c-io=0.14.18=h33ff4e5_10
-  - aws-c-mqtt=0.10.6=h02abb05_0
-  - aws-c-s3=0.6.6=h834ce55_0
-  - aws-c-sdkutils=0.1.19=h756ea98_3
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-  - azure-core-cpp=1.13.0=h935415a_0
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-  - azure-storage-common-cpp=12.7.0=h10ac4d7_1
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-  - google-cloud-sdk=493.0.0=py312h7900ff3_0
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-  - sparse=0.15.4=pyhd8ed1ab_0
-  - spdlog=1.14.1=hed91bc2_1
-  - spectate=1.0.1=pyhd8ed1ab_0
-  - sphinx=7.4.7=pyhd8ed1ab_0
-  - sphinx-autobuild=2024.9.19=pyhd8ed1ab_0
-  - sphinx-book-theme=1.1.3=pyhd8ed1ab_0
-  - sphinx-comments=0.0.3=pyh9f0ad1d_0
-  - sphinx-copybutton=0.5.2=pyhd8ed1ab_0
-  - sphinx-design=0.6.1=pyhd8ed1ab_1
-  - sphinx-external-toc=1.0.1=pyhd8ed1ab_0
-  - sphinx-jupyterbook-latex=1.0.0=pyhd8ed1ab_0
-  - sphinx-multitoc-numbering=0.1.3=pyhd8ed1ab_0
-  - sphinx-thebe=0.3.1=pyhd8ed1ab_0
-  - sphinx-togglebutton=0.3.2=pyhd8ed1ab_0
-  - sphinxcontrib-applehelp=2.0.0=pyhd8ed1ab_0
-  - sphinxcontrib-bibtex=2.6.3=pyhd8ed1ab_0
-  - sphinxcontrib-devhelp=2.0.0=pyhd8ed1ab_0
-  - sphinxcontrib-htmlhelp=2.1.0=pyhd8ed1ab_0
-  - sphinxcontrib-jsmath=1.0.1=pyhd8ed1ab_0
-  - sphinxcontrib-qthelp=2.0.0=pyhd8ed1ab_0
-  - sphinxcontrib-serializinghtml=1.1.10=pyhd8ed1ab_0
-  - sqlalchemy=2.0.35=py312h66e93f0_0
-  - sqlite=3.46.1=h9eae976_0
-  - stack_data=0.6.2=pyhd8ed1ab_0
-  - starlette=0.39.0=pyhd8ed1ab_0
-  - statsmodels=0.14.3=py312hc0a28a1_1
-  - streamlit=1.38.0=pyhd8ed1ab_0
-  - svgwrite=1.4.3=pyhd8ed1ab_0
-  - svt-av1=2.2.1=h5888daf_0
-  - sympy=1.13.2=pypyh2585a3b_103
-  - sysroot_linux-64=2.17=h4a8ded7_16
-  - tabulate=0.9.0=pyhd8ed1ab_1
-  - tbb=2021.13.0=h84d6215_0
-  - tblib=3.0.0=pyhd8ed1ab_0
-  - tenacity=8.5.0=pyhd8ed1ab_0
-  - terminado=0.18.1=pyh0d859eb_0
-  - threadpoolctl=3.5.0=pyhc1e730c_0
-  - throttler=1.2.2=pyhd8ed1ab_0
-  - tifffile=2024.8.30=pyhd8ed1ab_0
-  - tiledb=2.26.1=h4c922dd_1
-  - tinycss2=1.3.0=pyhd8ed1ab_0
-  - tk=8.6.13=noxft_h4845f30_101
-  - toml=0.10.2=pyhd8ed1ab_0
-  - tomli=2.0.1=pyhd8ed1ab_0
-  - toolz=0.12.1=pyhd8ed1ab_0
-  - toposort=1.10=pyhd8ed1ab_0
-  - tornado=6.4.1=py312h66e93f0_1
-  - tqdm=4.66.5=pyhd8ed1ab_0
-  - traitlets=5.14.3=pyhd8ed1ab_0
-  - traittypes=0.2.1=pyh9f0ad1d_2
-  - tskit=0.5.8=py312hc0a28a1_1
-  - types-python-dateutil=2.9.0.20240906=pyhd8ed1ab_0
-  - typing-extensions=4.12.2=hd8ed1ab_0
-  - typing_extensions=4.12.2=pyha770c72_0
-  - typing_utils=0.1.0=pyhd8ed1ab_0
-  - tzcode=2024b=hb9d3cd8_0
-  - tzdata=2024a=h8827d51_1
-  - tzlocal=5.2=py312h7900ff3_1
-  - ubiquerg=0.8.0=pyhd8ed1ab_0
-  - uc-micro-py=1.0.3=pyhd8ed1ab_0
-  - umap-learn=0.5.6=py312h7900ff3_1
-  - uncertainties=3.2.2=pyhd8ed1ab_1
-  - uri-template=1.3.0=pyhd8ed1ab_0
-  - uriparser=0.9.8=hac33072_0
-  - urllib3=2.2.3=pyhd8ed1ab_0
-  - uvicorn=0.30.6=py312h7900ff3_0
-  - validators=0.34.0=pyhd8ed1ab_0
-  - veracitools=0.1.3=py_0
-  - voila=0.4.5=pyhd8ed1ab_0
-  - voila-gridstack=0.3.1=pyhd8ed1ab_1
-  - watchdog=4.0.1=py312h7900ff3_0
-  - watchfiles=0.24.0=py312h12e396e_1
-  - wayland=1.23.1=h3e06ad9_0
-  - wcwidth=0.2.13=pyhd8ed1ab_0
-  - webcolors=24.8.0=pyhd8ed1ab_0
-  - webencodings=0.5.1=pyhd8ed1ab_2
-  - websocket-client=1.8.0=pyhd8ed1ab_0
-  - websockets=13.1=py312h66e93f0_0
-  - werkzeug=3.0.4=pyhd8ed1ab_0
-  - wheel=0.44.0=pyhd8ed1ab_0
-  - widgetsnbextension=3.5.1=pyh9f0ad1d_3
-  - wrapt=1.16.0=py312h66e93f0_1
-  - xarray=2024.7.0=pyhd8ed1ab_0
-  - xcb-util=0.4.1=hb711507_2
-  - xcb-util-cursor=0.1.5=hb9d3cd8_0
-  - xcb-util-image=0.4.0=hb711507_2
-  - xcb-util-keysyms=0.4.1=hb711507_0
-  - xcb-util-renderutil=0.3.10=hb711507_0
-  - xcb-util-wm=0.4.2=hb711507_0
-  - xerces-c=3.2.5=h666cd97_1
-  - xkeyboard-config=2.42=h4ab18f5_0
-  - xlrd=2.0.1=pyhd8ed1ab_3
-  - xlwt=1.3.0=py_1
-  - xorg-fixesproto=5.0=hb9d3cd8_1003
-  - xorg-inputproto=2.3.2=hb9d3cd8_1003
-  - xorg-kbproto=1.0.7=hb9d3cd8_1003
-  - xorg-libice=1.1.1=hd590300_0
-  - xorg-libsm=1.2.4=h7391055_0
-  - xorg-libx11=1.8.9=hb711507_1
-  - xorg-libxau=1.0.11=hb9d3cd8_1
-  - xorg-libxdmcp=1.1.3=hb9d3cd8_1
-  - xorg-libxext=1.3.4=h0b41bf4_2
-  - xorg-libxfixes=5.0.3=h7f98852_1004
-  - xorg-libxi=1.7.10=h4bc722e_1
-  - xorg-libxrender=0.9.11=hd590300_0
-  - xorg-libxtst=1.2.5=h4bc722e_0
-  - xorg-libxxf86vm=1.1.5=hb9d3cd8_2
-  - xorg-recordproto=1.14.2=hb9d3cd8_1003
-  - xorg-renderproto=0.11.1=hb9d3cd8_1003
-  - xorg-xextproto=7.3.0=hb9d3cd8_1004
-  - xorg-xproto=7.0.31=hb9d3cd8_1008
-  - xyzservices=2024.9.0=pyhd8ed1ab_0
-  - xz=5.2.6=h166bdaf_0
-  - yaml=0.2.5=h7f98852_2
-  - yarl=1.9.4=py312h66e93f0_1
-  - yte=1.5.4=pyha770c72_0
-  - zarr=2.15.0=pyhd8ed1ab_1
-  - zeromq=4.3.5=ha4adb4c_5
-  - zfp=1.0.1=h5888daf_2
-  - zict=3.0.0=pyhd8ed1ab_0
-  - zipp=3.20.2=pyhd8ed1ab_0
-  - zlib=1.3.1=h4ab18f5_1
-  - zlib-ng=2.2.2=h5888daf_0
-  - zstandard=0.23.0=py312hef9b889_1
-  - zstd=1.5.6=ha6fb4c9_0
-  - pip:
-      - biotite==1.0.1
-      - biotraj==1.2.1
-      - dash-core-components==2.0.0
-      - dash-cytoscape==1.0.2
-      - dash-html-components==2.0.0
-      - dash-table==5.0.0
-      - igv-notebook==0.5.2
-      - ipinfo==5.1.1
-      - lxml==5.3.0
-      - lxml-html-clean==0.2.2
-      - malariagen-data==13.2.1
-      - numpydoc-decorator==2.2.1
-      - orjson==3.10.7
-      - petlx==1.0.3
-      - protopunica==0.14.8.post2
-      - pyerf==1.0.1
-      - pyfaidx==0.8.1.2
-      - python-gist==0.10.6
-      - python-gnupg==0.4.9
-      - scikit-allel==1.3.13
-      - scikits-bootstrap==1.1.0
-      - sgkit==0.9.0
-      - sh==2.0.7
-      - termcolor==2.3.0
-      - typeguard==4.3.0
-      - yaspin==3.1.0
-prefix: /home/runner/work/mgenv/mgenv/deps/conda/envs/mgenv-24fa320

From 7ae1207c9d444778702b241c29cbeef6cff15310 Mon Sep 17 00:00:00 2001
From: _ <4256466+leehart@users.noreply.github.com>
Date: Thu, 14 Nov 2024 11:15:13 -0600
Subject: [PATCH 4/8] Update environment.yml symlink

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index ff9e5d1..82c62a3 120000
--- a/environment.yml
+++ b/environment.yml
@@ -1 +1 @@
-environment-pinned-linux.yml
\ No newline at end of file
+environment-pinned-ubuntu-latest.yml
\ No newline at end of file

From d1b6736ccd96b53003ecacc1e496dd5dcfa258c0 Mon Sep 17 00:00:00 2001
From: _ <4256466+leehart@users.noreply.github.com>
Date: Thu, 14 Nov 2024 11:18:24 -0600
Subject: [PATCH 5/8] WIP: diagnostic: reproduce error

---
 install-conda.sh | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/install-conda.sh b/install-conda.sh
index 77f32e5..23810c9 100755
--- a/install-conda.sh
+++ b/install-conda.sh
@@ -83,5 +83,9 @@ if [ -f "$ENVPINNED" ]; then
 
 else
     echo "not got pinned"
-
+    # Here we rebuild the environment from the unpinned requirements files,
+    # which is what a maintainer will do when they want to upgrade the pinned
+    # definition files.
+    echo "[mgenv] going to try removing $CONDANAME"
+    conda env remove -v --name=$CONDANAME
 fi

From 726d7a9d9184876b673664aa753f6665ced9b4c7 Mon Sep 17 00:00:00 2001
From: _ <4256466+leehart@users.noreply.github.com>
Date: Fri, 15 Nov 2024 03:05:34 -0600
Subject: [PATCH 6/8] Avoid raising EnvironmentLocationNotFound when trying to
 remove old conda env

---
 install-conda.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install-conda.sh b/install-conda.sh
index 23810c9..f62e195 100755
--- a/install-conda.sh
+++ b/install-conda.sh
@@ -87,5 +87,5 @@ else
     # which is what a maintainer will do when they want to upgrade the pinned
     # definition files.
     echo "[mgenv] going to try removing $CONDANAME"
-    conda env remove -v --name=$CONDANAME
+    conda env remove -v --name="$CONDANAME" || true
 fi

From 8ffa0982703bb1add724b47411a5ca5451ec4140 Mon Sep 17 00:00:00 2001
From: _ <4256466+leehart@users.noreply.github.com>
Date: Fri, 15 Nov 2024 03:37:13 -0600
Subject: [PATCH 7/8] Reinstate install-conda code w/
 EnvironmentLocationNotFound avoidance

---
 install-conda.sh | 26 +++++++++++++++++++++-----
 1 file changed, 21 insertions(+), 5 deletions(-)

diff --git a/install-conda.sh b/install-conda.sh
index f62e195..1e10526 100755
--- a/install-conda.sh
+++ b/install-conda.sh
@@ -79,13 +79,29 @@ fi
 ENVPINNED=${MGENVDIR}/environment-pinned-${OS}.yml
 
 if [ -f "$ENVPINNED" ]; then
-    echo "got pinned"
+    # Here we build the environment from the pinned definition file,
+    # this is what we expect users to do.
+    echo "[mgenv] creating environment $CONDANAME from $ENVPINNED"
+    conda env create -v --yes --name $CONDANAME --file $ENVPINNED
 
 else
-    echo "not got pinned"
     # Here we rebuild the environment from the unpinned requirements files,
     # which is what a maintainer will do when they want to upgrade the pinned
     # definition files.
-    echo "[mgenv] going to try removing $CONDANAME"
-    conda env remove -v --name="$CONDANAME" || true
-fi
+    conda env remove -v --name=$CONDANAME || true
+    echo "[mgenv] recreating $ENVPINNED"
+    echo "[mgenv] installing conda packages"
+    conda create --yes -v --strict-channel-priority $CHANNEL_OPTS --name $CONDANAME --file ${MGENVDIR}/requirements-conda.txt --file ${MGENVDIR}/requirements-compilers-${OS}.txt
+    echo "[mgenv] installing packages from pypi"
+    source activate $CONDANAME
+    pip install -v -r ${MGENVDIR}/requirements-pypi.txt
+    echo "[mgenv] exporting environment"
+    # N.B., here we add the conda-forge/label/broken channel so that the install
+    # will still work in the future, even if some conda-forge packages have been
+    # moved to the broken channel.
+    conda env export -v $CHANNEL_OPTS --channel=conda-forge/label/broken --name=$CONDANAME > $ENVPINNED
+    echo "*** $ENVPINNED ***"
+    cat $ENVPINNED
+    echo "*** $ENVPINNED ***"
+
+fi
\ No newline at end of file

From fe42d7343b8b539ab752c87bb6a8ae5a75a42d1e Mon Sep 17 00:00:00 2001
From: _ <4256466+leehart@users.noreply.github.com>
Date: Fri, 15 Nov 2024 04:01:49 -0600
Subject: [PATCH 8/8] Add reproduced pinned env files

---
 environment-pinned-macos-latest.yml  | 714 +++++++++++++++++++++++++
 environment-pinned-ubuntu-latest.yml | 757 +++++++++++++++++++++++++++
 2 files changed, 1471 insertions(+)
 create mode 100644 environment-pinned-macos-latest.yml
 create mode 100644 environment-pinned-ubuntu-latest.yml

diff --git a/environment-pinned-macos-latest.yml b/environment-pinned-macos-latest.yml
new file mode 100644
index 0000000..efead7b
--- /dev/null
+++ b/environment-pinned-macos-latest.yml
@@ -0,0 +1,714 @@
+name: binder-6cbd385
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+  - conda-forge/label/broken
+dependencies:
+  - accessible-pygments=0.0.4=pyhd8ed1ab_0
+  - affine=2.4.0=pyhd8ed1ab_0
+  - aiobotocore=2.13.0=pyhd8ed1ab_0
+  - aioeasywebdav=2.4.0=pyha770c72_0
+  - aiofiles=22.1.0=pyhd8ed1ab_0
+  - aiohttp=3.9.5=py310hb372a2b_0
+  - aioitertools=0.11.0=pyhd8ed1ab_0
+  - aiosignal=1.3.1=pyhd8ed1ab_0
+  - aiosqlite=0.20.0=pyhd8ed1ab_0
+  - alabaster=0.7.16=pyhd8ed1ab_0
+  - almosthere=2.0.2=h05e3726_1
+  - altair=5.3.0=pyhd8ed1ab_0
+  - amply=0.1.6=pyhd8ed1ab_0
+  - anyio=3.7.1=pyhd8ed1ab_0
+  - aom=3.9.0=h9bc2f43_0
+  - appdirs=1.4.4=pyh9f0ad1d_0
+  - appnope=0.1.4=pyhd8ed1ab_0
+  - apricot-select=0.6.1=pyhd8ed1ab_0
+  - argon2-cffi=23.1.0=pyhd8ed1ab_0
+  - argon2-cffi-bindings=21.2.0=py310h6729b98_4
+  - arrow=1.3.0=pyhd8ed1ab_0
+  - asciitree=0.3.3=py_2
+  - asteval=0.9.33=pyhd8ed1ab_0
+  - asttokens=2.4.1=pyhd8ed1ab_0
+  - async-timeout=4.0.3=pyhd8ed1ab_0
+  - atk-1.0=2.38.0=h4bec284_2
+  - attmap=0.13.2=pyhd8ed1ab_0
+  - attrs=23.2.0=pyh71513ae_0
+  - aws-c-auth=0.7.22=h26aba2d_2
+  - aws-c-cal=0.6.14=hb0e519c_1
+  - aws-c-common=0.9.19=hfdf4475_0
+  - aws-c-compression=0.2.18=hb0e519c_6
+  - aws-c-event-stream=0.4.2=hc5e814a_12
+  - aws-c-http=0.8.1=ha6e9f73_17
+  - aws-c-io=0.14.8=hf69683f_5
+  - aws-c-mqtt=0.10.4=h76e2169_4
+  - aws-c-s3=0.5.9=hd10324c_3
+  - aws-c-sdkutils=0.1.16=hb0e519c_2
+  - aws-checksums=0.1.18=hb0e519c_6
+  - aws-crt-cpp=0.26.9=h473fab1_0
+  - aws-sdk-cpp=1.11.329=h6b2b1af_3
+  - azure-core-cpp=1.11.1=hbb1e571_1
+  - azure-identity-cpp=1.6.0=h9a80fee_1
+  - azure-storage-blobs-cpp=12.10.0=h7728843_1
+  - azure-storage-common-cpp=12.5.0=h0e82ce4_4
+  - babel=2.14.0=pyhd8ed1ab_0
+  - bcftools=1.20=h79774e1_0
+  - bcrypt=4.1.3=py310h12a1ced_0
+  - beautifulsoup4=4.12.3=pyha770c72_0
+  - bed-reader=1.0.0=py310hdd6081d_0
+  - bgen=4.1.3=ha41cdc6_0
+  - biopython=1.83=py310hb372a2b_0
+  - black=24.4.2=py310h2ec42d9_0
+  - blas=2.122=openblas
+  - blas-devel=3.9.0=22_osx64_openblas
+  - bleach=6.1.0=pyhd8ed1ab_0
+  - blinker=1.8.2=pyhd8ed1ab_0
+  - blosc=1.21.5=hafa3907_1
+  - bokeh=3.4.1=pyhd8ed1ab_0
+  - boto3=1.34.106=pyhd8ed1ab_0
+  - botocore=1.34.106=pyge310_1234567_0
+  - bqplot=0.12.43=pyhd8ed1ab_0
+  - branca=0.7.2=pyhd8ed1ab_0
+  - brotli=1.1.0=h0dc2134_1
+  - brotli-bin=1.1.0=h0dc2134_1
+  - brotli-python=1.1.0=py310h9e9d8ca_1
+  - brunsli=0.1=h046ec9c_0
+  - bzip2=1.0.8=h10d778d_5
+  - c-ares=1.28.1=h10d778d_0
+  - c-blosc2=2.14.4=h0ae8482_1
+  - ca-certificates=2024.6.2=h8857fd0_0
+  - cached-property=1.5.2=hd8ed1ab_1
+  - cached_property=1.5.2=pyha770c72_1
+  - cachetools=5.3.3=pyhd8ed1ab_0
+  - cairo=1.18.0=h99e66fa_0
+  - cartopy=0.23.0=py310hbf2a7f0_1
+  - cbgen=1.0.1=py310h1961e1f_2
+  - cctools_osx-64=986=h58a35ae_0
+  - certifi=2024.2.2=pyhd8ed1ab_0
+  - cffi=1.16.0=py310hdca579f_0
+  - cfitsio=4.4.0=h60fb419_1
+  - cftime=1.6.3=py310hde789be_1
+  - charls=2.4.2=he965462_0
+  - charset-normalizer=3.3.2=pyhd8ed1ab_0
+  - clang=18.1.6=default_ha3b9224_0
+  - clang-18=18.1.6=default_ha3b9224_0
+  - clang_impl_osx-64=18.1.6=h2ef7af4_15
+  - clang_osx-64=18.1.6=hb91bd55_15
+  - clangxx=18.1.6=default_ha3b9224_0
+  - clangxx_impl_osx-64=18.1.6=hfd204e2_15
+  - clangxx_osx-64=18.1.6=hb91bd55_15
+  - click=8.1.7=unix_pyh707e725_0
+  - click-plugins=1.1.1=py_0
+  - cligj=0.7.2=pyhd8ed1ab_1
+  - cloudpickle=3.0.0=pyhd8ed1ab_0
+  - coin-or-cbc=2.10.11=h6ddf826_0
+  - coin-or-cgl=0.60.7=ha3c4b8c_0
+  - coin-or-clp=1.17.8=hf0ee74e_0
+  - coin-or-osi=0.108.10=h13a241d_0
+  - coin-or-utils=2.11.11=h86ddba1_0
+  - coincbc=2.10.11=0_metapackage
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - colorcet=3.1.0=pyhd8ed1ab_0
+  - comm=0.2.2=pyhd8ed1ab_0
+  - compiler-rt=18.1.6=h734a56e_0
+  - compiler-rt_osx-64=18.1.6=h7312ed1_0
+  - configargparse=1.7=pyhd8ed1ab_0
+  - connection_pool=0.0.3=pyhd3deb0d_0
+  - contourpy=1.2.1=py310hb3b189b_0
+  - coverage=7.5.3=py310h936d840_0
+  - cramjam=2.8.3=py310hd8ae0ce_0
+  - cryptography=42.0.8=py310h8d695f1_0
+  - cycler=0.12.1=pyhd8ed1ab_0
+  - cython=3.0.10=py310h5daac23_0
+  - cytoolz=0.12.3=py310hb372a2b_0
+  - dash=2.17.0=pyhd8ed1ab_0
+  - dask=2024.5.2=pyhd8ed1ab_0
+  - dask-core=2024.5.2=pyhd8ed1ab_0
+  - dask-expr=1.1.2=pyhd8ed1ab_0
+  - dask-gateway=2022.10.0=pyh8af1aa0_0
+  - dask-glm=0.3.2=pyhd8ed1ab_0
+  - dask-ml=2024.3.20=pyhd8ed1ab_0
+  - dataclasses=0.8=pyhc8e2a94_3
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+  - psutil=5.9.8=py310hb372a2b_0
+  - pthread-stubs=0.4=hc929b4f_1001
+  - ptyprocess=0.7.0=pyhd3deb0d_0
+  - pulp=2.7.0=py310h2ec42d9_1
+  - pure_eval=0.2.2=pyhd8ed1ab_0
+  - py-cpuinfo=9.0.0=pyhd8ed1ab_0
+  - py2vega=0.6.1=pyhd8ed1ab_0
+  - pyarrow=16.1.0=py310h1cef2ca_1
+  - pyarrow-core=16.1.0=py310h907dfef_1_cpu
+  - pyarrow-hotfix=0.6=pyhd8ed1ab_0
+  - pyasn1=0.6.0=pyhd8ed1ab_0
+  - pyasn1-modules=0.4.0=pyhd8ed1ab_0
+  - pybtex=0.24.0=pyhd8ed1ab_2
+  - pybtex-docutils=1.0.3=py310h2ec42d9_1
+  - pycodestyle=2.11.1=pyhd8ed1ab_0
+  - pycountry=22.3.5=pyhd8ed1ab_0
+  - pycparser=2.22=pyhd8ed1ab_0
+  - pyct=0.5.0=pyhd8ed1ab_0
+  - pydata-sphinx-theme=0.15.3=pyhd8ed1ab_0
+  - pydeck=0.8.0=pyhd8ed1ab_0
+  - pyflakes=3.2.0=pyhd8ed1ab_0
+  - pygments=2.18.0=pyhd8ed1ab_0
+  - pyjwt=2.8.0=pyhd8ed1ab_1
+  - pynacl=1.5.0=py310h6729b98_3
+  - pynndescent=0.5.12=pyhca7485f_0
+  - pyobjc-core=10.2=py310h3674b6a_0
+  - pyobjc-framework-cocoa=10.2=py310h3674b6a_0
+  - pyopenssl=24.0.0=pyhd8ed1ab_0
+  - pyparsing=3.1.2=pyhd8ed1ab_0
+  - pyproj=3.6.1=py310h5c96a55_6
+  - pyprojroot=0.3.0=pyhd8ed1ab_0
+  - pysftp=0.2.9=py_1
+  - pyshp=2.3.1=pyhd8ed1ab_0
+  - pysocks=1.7.1=pyha2e5f31_6
+  - pytables=3.9.2=py310hea8cab2_2
+  - pytest=8.2.2=pyhd8ed1ab_0
+  - pytest-cov=5.0.0=pyhd8ed1ab_0
+  - python=3.10.14=h00d2728_0_cpython
+  - python-dateutil=2.9.0=pyhd8ed1ab_0
+  - python-fastjsonschema=2.19.1=pyhd8ed1ab_0
+  - python-graphviz=0.20.3=pyh717bed2_0
+  - python-irodsclient=2.0.1=pyhd8ed1ab_0
+  - python-json-logger=2.0.7=pyhd8ed1ab_0
+  - python-magic=0.4.27=py310h2ec42d9_4
+  - python-tzdata=2024.1=pyhd8ed1ab_0
+  - python_abi=3.10=4_cp310
+  - pytorch=2.3.0=cpu_mkl_py310heb6a33a_101
+  - pytz=2024.1=pyhd8ed1ab_0
+  - pyu2f=0.1.5=pyhd8ed1ab_0
+  - pyviz_comms=2.3.2=pyhd8ed1ab_0
+  - pywavelets=1.4.1=py310hf0b6da5_1
+  - pyyaml=6.0.1=py310h6729b98_1
+  - pyzmq=26.0.3=py310he0bbd50_0
+  - qtconsole-base=5.5.2=pyha770c72_0
+  - qtpy=2.4.1=pyhd8ed1ab_0
+  - rasterio=1.3.10=py310he82d439_3
+  - rav1e=0.6.6=h7205ca4_2
+  - re2=2023.09.01=hb168e87_2
+  - readline=8.2=h9e318b2_1
+  - rechunker=0.5.2=pyhd8ed1ab_1
+  - referencing=0.35.1=pyhd8ed1ab_0
+  - requests=2.32.3=pyhd8ed1ab_0
+  - requests-oauthlib=2.0.0=pyhd8ed1ab_0
+  - reretry=0.11.8=pyhd8ed1ab_0
+  - retrying=1.3.3=py_2
+  - rfc3339-validator=0.1.4=pyhd8ed1ab_0
+  - rfc3986-validator=0.1.1=pyh9f0ad1d_0
+  - rich=13.7.1=pyhd8ed1ab_0
+  - rioxarray=0.15.5=pyhd8ed1ab_0
+  - rpds-py=0.18.1=py310h12a1ced_0
+  - rsa=4.9=pyhd8ed1ab_0
+  - rtree=1.2.0=py310had9ce37_0
+  - ruamel.yaml=0.18.6=py310hb372a2b_0
+  - ruamel.yaml.clib=0.2.8=py310hb372a2b_0
+  - s3cmd=2.0.2=py_0
+  - s3fs=2024.6.0=pyhd8ed1ab_0
+  - s3transfer=0.10.1=pyhd8ed1ab_0
+  - samtools=1.20=hd510865_0
+  - scikit-allel=1.3.8=py310hc47d138_1
+  - scikit-image=0.23.2=py310hc47d138_0
+  - scikit-learn=1.5.0=py310h9d65eca_1
+  - scipy=1.13.1=py310h35d8cac_0
+  - seaborn=0.13.2=hd8ed1ab_2
+  - seaborn-base=0.13.2=pyhd8ed1ab_2
+  - send2trash=1.8.3=pyh31c8845_0
+  - setuptools=70.0.0=pyhd8ed1ab_0
+  - setuptools-scm=8.1.0=pyhd8ed1ab_0
+  - sgkit=0.8.0=pyhd8ed1ab_0
+  - shapely=2.0.4=py310hb54ad17_1
+  - sigtool=0.1.3=h88f4db0_0
+  - six=1.16.0=pyh6c4a22f_0
+  - slacker=0.14.0=py_0
+  - sleef=3.5.1=h6db0672_2
+  - smart_open=7.0.4=pyhd8ed1ab_0
+  - smmap=5.0.0=pyhd8ed1ab_0
+  - snakemake=7.32.4=hdfd78af_1
+  - snakemake-minimal=7.32.4=pyhdfd78af_1
+  - snappy=1.2.0=h6dc393e_1
+  - sniffio=1.3.1=pyhd8ed1ab_0
+  - snowballstemmer=2.2.0=pyhd8ed1ab_0
+  - snuggs=1.4.7=py_0
+  - sortedcontainers=2.4.0=pyhd8ed1ab_0
+  - soupsieve=2.5=pyhd8ed1ab_1
+  - sparse=0.15.4=pyhd8ed1ab_0
+  - spdlog=1.13.0=h1a4aec9_0
+  - spectate=1.0.1=pyhd8ed1ab_0
+  - sphinx=7.3.7=pyhd8ed1ab_0
+  - sphinx-autobuild=2024.4.16=pyhd8ed1ab_0
+  - sphinx-book-theme=1.1.2=pyhd8ed1ab_0
+  - sphinx-comments=0.0.3=pyh9f0ad1d_0
+  - sphinx-copybutton=0.5.2=pyhd8ed1ab_0
+  - sphinx-design=0.5.0=pyhd8ed1ab_0
+  - sphinx-external-toc=1.0.1=pyhd8ed1ab_0
+  - sphinx-jupyterbook-latex=1.0.0=pyhd8ed1ab_0
+  - sphinx-multitoc-numbering=0.1.3=pyhd8ed1ab_0
+  - sphinx-thebe=0.3.1=pyhd8ed1ab_0
+  - sphinx-togglebutton=0.3.2=pyhd8ed1ab_0
+  - sphinxcontrib-applehelp=1.0.8=pyhd8ed1ab_0
+  - sphinxcontrib-bibtex=2.6.2=pyhd8ed1ab_0
+  - sphinxcontrib-devhelp=1.0.6=pyhd8ed1ab_0
+  - sphinxcontrib-htmlhelp=2.0.5=pyhd8ed1ab_0
+  - sphinxcontrib-jsmath=1.0.1=pyhd8ed1ab_0
+  - sphinxcontrib-qthelp=1.0.7=pyhd8ed1ab_0
+  - sphinxcontrib-serializinghtml=1.1.10=pyhd8ed1ab_0
+  - sqlalchemy=2.0.30=py310h56a41de_0
+  - sqlite=3.45.3=h7461747_0
+  - stack_data=0.6.2=pyhd8ed1ab_0
+  - starlette=0.37.2=pyhd8ed1ab_0
+  - statsmodels=0.14.2=py310hde789be_0
+  - stone=3.3.2=pyhd8ed1ab_0
+  - stopit=1.1.2=py_0
+  - streamlit=1.35.0=pyhd8ed1ab_0
+  - svgwrite=1.4.3=pyhd8ed1ab_0
+  - svt-av1=2.1.0=hf036a51_0
+  - sympy=1.12=pypyh9d50eac_103
+  - tabulate=0.9.0=pyhd8ed1ab_1
+  - tapi=1100.0.11=h9ce4665_0
+  - tbb=2021.12.0=h3c5361c_1
+  - tblib=3.0.0=pyhd8ed1ab_0
+  - tenacity=8.3.0=pyhd8ed1ab_0
+  - terminado=0.18.1=pyh31c8845_0
+  - threadpoolctl=3.5.0=pyhc1e730c_0
+  - throttler=1.2.2=pyhd8ed1ab_0
+  - tifffile=2024.5.22=pyhd8ed1ab_0
+  - tiledb=2.23.0=h7f463ff_2
+  - tinycss2=1.3.0=pyhd8ed1ab_0
+  - tk=8.6.13=h1abcd95_1
+  - toml=0.10.2=pyhd8ed1ab_0
+  - tomli=2.0.1=pyhd8ed1ab_0
+  - toolz=0.12.1=pyhd8ed1ab_0
+  - toposort=1.10=pyhd8ed1ab_0
+  - tornado=6.4.1=py310h936d840_0
+  - tqdm=4.66.4=pyhd8ed1ab_0
+  - traitlets=5.14.3=pyhd8ed1ab_0
+  - traittypes=0.2.1=pyh9f0ad1d_2
+  - tskit=0.5.6=py310hde789be_2
+  - types-python-dateutil=2.9.0.20240316=pyhd8ed1ab_0
+  - typing-extensions=4.12.1=hd8ed1ab_0
+  - typing_extensions=4.12.1=pyha770c72_0
+  - tzcode=2024a=h10d778d_0
+  - tzdata=2024a=h0c530f3_0
+  - tzlocal=5.2=py310h2ec42d9_0
+  - ubiquerg=0.7.0=pyhd8ed1ab_0
+  - uc-micro-py=1.0.3=pyhd8ed1ab_0
+  - umap-learn=0.5.5=py310h2ec42d9_1
+  - uncertainties=3.2.0=pyhd8ed1ab_0
+  - unicodedata2=15.1.0=py310h6729b98_0
+  - uri-template=1.3.0=pyhd8ed1ab_0
+  - uriparser=0.9.8=h6aefe2f_0
+  - uritemplate=4.1.1=pyhd8ed1ab_0
+  - urllib3=2.2.1=pyhd8ed1ab_0
+  - uvicorn=0.30.1=py310h2ec42d9_0
+  - validators=0.28.3=pyhd8ed1ab_0
+  - veracitools=0.1.3=py_0
+  - voila=0.3.8=pyhd8ed1ab_0
+  - voila-gridstack=0.3.1=pyhd8ed1ab_1
+  - watchdog=4.0.1=py310h936d840_0
+  - watchfiles=0.22.0=py310h12a1ced_0
+  - wcwidth=0.2.13=pyhd8ed1ab_0
+  - webcolors=24.6.0=pyhd8ed1ab_0
+  - webencodings=0.5.1=pyhd8ed1ab_2
+  - websocket-client=1.8.0=pyhd8ed1ab_0
+  - websockets=12.0=py310hb372a2b_0
+  - werkzeug=3.0.3=pyhd8ed1ab_0
+  - wheel=0.43.0=pyhd8ed1ab_1
+  - widgetsnbextension=3.5.2=py310h2ec42d9_1
+  - wrapt=1.16.0=py310hb372a2b_0
+  - xarray=2024.5.0=pyhd8ed1ab_0
+  - xerces-c=3.2.5=hbbe9ea5_0
+  - xlrd=2.0.1=pyhd8ed1ab_3
+  - xlwt=1.3.0=py_1
+  - xorg-libxau=1.0.11=h0dc2134_0
+  - xorg-libxdmcp=1.1.3=h35c211d_0
+  - xyzservices=2024.6.0=pyhd8ed1ab_0
+  - xz=5.2.6=h775f41a_0
+  - y-py=0.5.9=py310hb28ce15_0
+  - yaml=0.2.5=h0d85af4_2
+  - yarl=1.9.4=py310hb372a2b_0
+  - ypy-websocket=0.8.2=pyhd8ed1ab_0
+  - yte=1.5.4=pyha770c72_0
+  - zarr=2.15.0=pyhd8ed1ab_1
+  - zeromq=4.3.5=hde137ed_4
+  - zfp=1.0.1=h295e98d_0
+  - zict=3.0.0=pyhd8ed1ab_0
+  - zipp=3.17.0=pyhd8ed1ab_0
+  - zlib=1.2.13=h87427d6_6
+  - zlib-ng=2.0.7=hb7f2c08_0
+  - zstd=1.5.6=h915ae27_0
+  - pip:
+      - biotite==0.40.0
+      - dash-core-components==2.0.0
+      - dash-cytoscape==1.0.1
+      - dash-html-components==2.0.0
+      - dash-table==5.0.0
+      - igv-notebook==0.5.2
+      - ipinfo==5.0.1
+      - lxml-html-clean==0.1.1
+      - malariagen-data==10.0.0
+      - numpydoc-decorator==2.2.0
+      - orjson==3.10.3
+      - petlx==1.0.3
+      - prettypandas==0.0.4
+      - protopunica==0.14.8.post1
+      - pyerf==1.0.1
+      - pyfaidx==0.8.1.1
+      - python-gist==0.10.6
+      - python-gnupg==0.4.9
+      - scikits-bootstrap==1.1.0
+      - sh==2.0.7
+      - termcolor==2.3.0
+      - typeguard==4.3.0
+      - yaspin==3.0.2
+prefix: /Users/runner/work/binder/binder/deps/conda/envs/binder-6cbd385
diff --git a/environment-pinned-ubuntu-latest.yml b/environment-pinned-ubuntu-latest.yml
new file mode 100644
index 0000000..07acae7
--- /dev/null
+++ b/environment-pinned-ubuntu-latest.yml
@@ -0,0 +1,757 @@
+name: binder-6cbd385
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+  - conda-forge/label/broken
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_kmp_llvm
+  - accessible-pygments=0.0.4=pyhd8ed1ab_0
+  - affine=2.4.0=pyhd8ed1ab_0
+  - aiobotocore=2.13.0=pyhd8ed1ab_0
+  - aioeasywebdav=2.4.0=pyha770c72_0
+  - aiofiles=22.1.0=pyhd8ed1ab_0
+  - aiohttp=3.9.5=py310h2372a71_0
+  - aioitertools=0.11.0=pyhd8ed1ab_0
+  - aiosignal=1.3.1=pyhd8ed1ab_0
+  - aiosqlite=0.20.0=pyhd8ed1ab_0
+  - alabaster=0.7.16=pyhd8ed1ab_0
+  - almosthere=2.0.2=h46c0cb4_1
+  - alsa-lib=1.2.11=hd590300_1
+  - altair=5.3.0=pyhd8ed1ab_0
+  - amply=0.1.6=pyhd8ed1ab_0
+  - anyio=3.7.1=pyhd8ed1ab_0
+  - aom=3.9.0=hac33072_0
+  - appdirs=1.4.4=pyh9f0ad1d_0
+  - apricot-select=0.6.1=pyhd8ed1ab_0
+  - argon2-cffi=23.1.0=pyhd8ed1ab_0
+  - argon2-cffi-bindings=21.2.0=py310h2372a71_4
+  - arrow=1.3.0=pyhd8ed1ab_0
+  - asciitree=0.3.3=py_2
+  - asteval=0.9.33=pyhd8ed1ab_0
+  - asttokens=2.4.1=pyhd8ed1ab_0
+  - async-timeout=4.0.3=pyhd8ed1ab_0
+  - atk-1.0=2.38.0=h04ea711_2
+  - attmap=0.13.2=pyhd8ed1ab_0
+  - attr=2.5.1=h166bdaf_1
+  - attrs=23.2.0=pyh71513ae_0
+  - aws-c-auth=0.7.22=h96bc93b_2
+  - aws-c-cal=0.6.14=h88a6e22_1
+  - aws-c-common=0.9.19=h4ab18f5_0
+  - aws-c-compression=0.2.18=h83b837d_6
+  - aws-c-event-stream=0.4.2=ha47c788_12
+  - aws-c-http=0.8.1=h29d6fba_17
+  - aws-c-io=0.14.8=h21d4f22_5
+  - aws-c-mqtt=0.10.4=h759edc4_4
+  - aws-c-s3=0.5.9=h594631b_3
+  - aws-c-sdkutils=0.1.16=h83b837d_2
+  - aws-checksums=0.1.18=h83b837d_6
+  - aws-crt-cpp=0.26.9=he3a8b3b_0
+  - aws-sdk-cpp=1.11.329=hba8bd5f_3
+  - azure-core-cpp=1.11.1=h91d86a7_1
+  - azure-identity-cpp=1.6.0=hf1915f5_1
+  - azure-storage-blobs-cpp=12.10.0=h00ab1b0_1
+  - azure-storage-common-cpp=12.5.0=h94269e2_4
+  - babel=2.14.0=pyhd8ed1ab_0
+  - bcftools=1.20=h8b25389_0
+  - bcrypt=4.1.3=py310he421c4c_0
+  - beautifulsoup4=4.12.3=pyha770c72_0
+  - bed-reader=1.0.0=py310h93aa1c4_0
+  - bgen=4.1.3=ha0ad84f_0
+  - binutils_impl_linux-64=2.40=ha1999f0_2
+  - binutils_linux-64=2.40=hdade7a5_3
+  - biopython=1.83=py310h2372a71_0
+  - black=24.4.2=py310hff52083_0
+  - blas=2.122=openblas
+  - blas-devel=3.9.0=22_linux64_openblas
+  - bleach=6.1.0=pyhd8ed1ab_0
+  - blinker=1.8.2=pyhd8ed1ab_0
+  - blosc=1.21.5=hc2324a3_1
+  - bokeh=3.4.1=pyhd8ed1ab_0
+  - boto3=1.34.106=pyhd8ed1ab_0
+  - botocore=1.34.106=pyge310_1234567_0
+  - bqplot=0.12.43=pyhd8ed1ab_0
+  - branca=0.7.2=pyhd8ed1ab_0
+  - brotli=1.1.0=hd590300_1
+  - brotli-bin=1.1.0=hd590300_1
+  - brotli-python=1.1.0=py310hc6cd4ac_1
+  - brunsli=0.1=h9c3ff4c_0
+  - bzip2=1.0.8=hd590300_5
+  - c-ares=1.28.1=hd590300_0
+  - c-blosc2=2.14.4=hb4ffafa_1
+  - ca-certificates=2024.6.2=hbcca054_0
+  - cached-property=1.5.2=hd8ed1ab_1
+  - cached_property=1.5.2=pyha770c72_1
+  - cachetools=5.3.3=pyhd8ed1ab_0
+  - cairo=1.18.0=h3faef2a_0
+  - cartopy=0.23.0=py310hf9f9076_1
+  - cbgen=1.0.1=py310h5764c6d_2
+  - certifi=2024.2.2=pyhd8ed1ab_0
+  - cffi=1.16.0=py310h2fee648_0
+  - cfitsio=4.4.0=hbdc6101_1
+  - cftime=1.6.3=py310h261611a_1
+  - charls=2.4.2=h59595ed_0
+  - charset-normalizer=3.3.2=pyhd8ed1ab_0
+  - click=8.1.7=unix_pyh707e725_0
+  - click-plugins=1.1.1=py_0
+  - cligj=0.7.2=pyhd8ed1ab_1
+  - cloudpickle=3.0.0=pyhd8ed1ab_0
+  - coin-or-cbc=2.10.11=h56f689f_0
+  - coin-or-cgl=0.60.7=h516709c_0
+  - coin-or-clp=1.17.8=h1ee7a9c_0
+  - coin-or-osi=0.108.10=haf5fa05_0
+  - coin-or-utils=2.11.11=hee58242_0
+  - coincbc=2.10.11=0_metapackage
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - colorcet=3.1.0=pyhd8ed1ab_0
+  - comm=0.2.2=pyhd8ed1ab_0
+  - configargparse=1.7=pyhd8ed1ab_0
+  - connection_pool=0.0.3=pyhd3deb0d_0
+  - contourpy=1.2.1=py310hd41b1e2_0
+  - coverage=7.5.3=py310hc51659f_0
+  - cramjam=2.8.3=py310hcb5633a_0
+  - cryptography=42.0.8=py310hb1bd9d3_0
+  - cycler=0.12.1=pyhd8ed1ab_0
+  - cython=3.0.10=py310hc6cd4ac_0
+  - cytoolz=0.12.3=py310h2372a71_0
+  - dash=2.17.0=pyhd8ed1ab_0
+  - dask=2024.5.2=pyhd8ed1ab_0
+  - dask-core=2024.5.2=pyhd8ed1ab_0
+  - dask-expr=1.1.2=pyhd8ed1ab_0
+  - dask-gateway=2022.10.0=pyh8af1aa0_0
+  - dask-glm=0.3.2=pyhd8ed1ab_0
+  - dask-ml=2024.3.20=pyhd8ed1ab_0
+  - dataclasses=0.8=pyhc8e2a94_3
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+  - sphinxcontrib-htmlhelp=2.0.5=pyhd8ed1ab_0
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+  - xarray=2024.5.0=pyhd8ed1ab_0
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+  - xorg-libsm=1.2.4=h7391055_0
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+  - xorg-libxau=1.0.11=hd590300_0
+  - xorg-libxdmcp=1.1.3=h7f98852_0
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+  - xorg-renderproto=0.11.1=h7f98852_1002
+  - xorg-xextproto=7.3.0=h0b41bf4_1003
+  - xorg-xf86vidmodeproto=2.3.1=h7f98852_1002
+  - xorg-xproto=7.0.31=h7f98852_1007
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+  - zeromq=4.3.5=h75354e8_4
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+  - zlib-ng=2.0.7=h0b41bf4_0
+  - zstd=1.5.6=ha6fb4c9_0
+  - pip:
+      - biotite==0.40.0
+      - dash-core-components==2.0.0
+      - dash-cytoscape==1.0.1
+      - dash-html-components==2.0.0
+      - dash-table==5.0.0
+      - igv-notebook==0.5.2
+      - ipinfo==5.0.1
+      - lxml-html-clean==0.1.1
+      - malariagen-data==10.0.0
+      - numpydoc-decorator==2.2.0
+      - orjson==3.10.3
+      - petlx==1.0.3
+      - prettypandas==0.0.4
+      - protopunica==0.14.8.post1
+      - pyerf==1.0.1
+      - pyfaidx==0.8.1.1
+      - python-gist==0.10.6
+      - python-gnupg==0.4.9
+      - scikits-bootstrap==1.1.0
+      - sh==2.0.7
+      - termcolor==2.3.0
+      - typeguard==4.3.0
+      - yaspin==3.0.2
+prefix: /home/runner/work/binder/binder/deps/conda/envs/binder-6cbd385