From 6c9cdbc40824881e0183d19d31b74117da132548 Mon Sep 17 00:00:00 2001
From: ctbus <ctbushman@gmail.com>
Date: Thu, 12 Oct 2023 11:14:57 -0400
Subject: [PATCH 1/7] Update version tag

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

diff --git a/install.sh b/install.sh
index d4175ea5..9e4b791d 100755
--- a/install.sh
+++ b/install.sh
@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
 __conda_url=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-__version_tag=$(if git describe --tags >/dev/null 2>&1 ; then git describe --tags; else echo v4.0.0; fi) # <--- Update this on each version release
+__version_tag=$(if git describe --tags >/dev/null 2>&1 ; then git describe --tags; else echo v4.1.0; fi) # <--- Update this on each version release
 __version_tag="${__version_tag:1}" # Remove the 'v' prefix
 
 read -r -d '' __usage <<-'EOF'

From 2b67593d890e46a4c0d888400bbb5ea3712f64ac Mon Sep 17 00:00:00 2001
From: ctbus <ctbushman@gmail.com>
Date: Thu, 12 Oct 2023 11:47:58 -0400
Subject: [PATCH 2/7] Update docs

---
 docs/structure.rst                  | 23 ++++----
 docs/usage.rst                      | 13 ++---
 src/sunbeamlib/tibanna_profile.yaml | 85 -----------------------------
 3 files changed, 15 insertions(+), 106 deletions(-)
 delete mode 100755 src/sunbeamlib/tibanna_profile.yaml

diff --git a/docs/structure.rst b/docs/structure.rst
index 71ab19a1..257ff1e0 100755
--- a/docs/structure.rst
+++ b/docs/structure.rst
@@ -26,7 +26,7 @@ sunbeam/ (root directory)
 -------------------------
 
 The root sunbeam directory holds a few important files including 
-``environment.yml``, ``setup.py``, and ``install.sh``. The environment file defines 
+``environment.yml``, ``pyproject.toml``, and ``install.sh``. The environment file defines 
 the dependencies required to run sunbeam and is used to create the main sunbeam 
 environment. The setup file defines the structure and dependencies of the 
 sunbeamlib_ and makes it installable via pip. The install script is used to install 
@@ -50,8 +50,7 @@ The additional files are all involved in the setup and deployment of the docs
 to ReadTheDocs using Sphinx. Most of these are autogenerated by Sphinx. The one 
 bit of trickiness comes from importing the version of sunbeam into the docs 
 build. This is done in ``conf.py`` by adding the sunbeam root to ``sys.path`` and 
-then importing ``sunbeamlib`` which stores the version tag in a ``__version__`` 
-variable using ``semantic_version``.
+then importing ``sunbeamlib`` which stores the version tag in ``__version__``.
 
 .. _envs:
 workflow/envs/
@@ -66,7 +65,7 @@ by default.
 
 The accompanying files named something like ``ENV_NAME.ARCH.pin.txt`` are generated 
 with ``snakedeploy``. They list all the packages and exact versions in a given 
-environment (and for the architecture they were generated on, e.g. linux-64) so that 
+environment (for the architecture they were generated on, e.g. linux-64) so that 
 snakemake can first try to use that exact environment and only if it fails, try to 
 solve the ``.yml`` file for itself.
 
@@ -93,14 +92,14 @@ rules. Again they are organized into subdirectories to match function and each
 is named according to the rule that calls it.
 
 .. _sunbeamlib:
-sunbeamlib/
+src/sunbeamlib/
 -----------
 
-This directory contains the python library that acts as a wrapper for 
-snakemake. The python files in the root contain a number of utility functions 
-whiles those in ``scripts/`` define the commands for sunbeam. 
-``scripts/command.py`` takes in ``sunbeam [cmd]`` and then routes it to the file 
-matching the given command. The ``data/`` directory contains the default config 
+This directory contains the python library that acts as a runner/utility for the 
+underlying snakemake. Many python files contain utility functions 
+whiles those prefixed by ``script_`` define the commands for sunbeam. 
+``script_sunbeam.py`` takes in ``sunbeam [cmd]`` and then routes it to the file 
+matching the given command. The ``.yml/.yaml`` data files include the default config 
 file as well as some sample config templates for running on a cluster. It also 
 contains the default profile template and one for slurm.
 
@@ -129,8 +128,8 @@ run by CircleCI as well as any scripts that are included in those jobs.
 
 This directory contains the ``PULL_REQUEST_TEMPLATE.md`` file which defines a 
 template for any pull requests on the sunbeam repository and ``ISSUE_TEMPLATE/`` 
-which contains issue templates for the repository. It is also where 
-the SuperLinter CI job definition lives.
+which contains issue templates for the repository. It is also where some
+CI job workflows live.
 
 .snakemake/
 ***********
diff --git a/docs/usage.rst b/docs/usage.rst
index 7daae8cf..b44e7a9a 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -77,13 +77,6 @@ installing or updating Sunbeam:
 If the tests fail, you should either refer to our troubleshooting guide or file
 an issue on our `Github page <https://github.com/sunbeam-labs/sunbeam/issues>`_.
 
-.. tip::
-
-  You can speed up the testing process by using the environment created during 
-  the install process with something like this 
-  'bash tests/run_tests.bash -e SUNBEAM_ENV_NAME'. Without this argument the 
-  script will create a temporary environment.
-
 .. _updating:
 Updating
 --------
@@ -101,9 +94,9 @@ upgrades, we will increment the patch or minor numbers (e.g. 1.0.0 ->
    git pull
    ./install.sh --upgrade all
 
-Sunbeam v3+ is designed to be installable separately on a system that already 
+Sunbeam is designed to be installable separately on a system that already 
 has sunbeam installed. This means multiple versions of sunbeam can be installed 
-on the same machine in different repositories.
+on the same machine in different repositories and different environments.
 
 .. _uninstall:
 Uninstalling or reinstalling
@@ -260,6 +253,8 @@ qc
   using cutadapt. Replace with ``""`` to skip.
 * ``cutadapt_opts``: (cutadapt) options to pass to cutadapt. Replace with ``""`` to pass no extra options.
 * ``kz_threshold``: a value between 0 and 1 to determine the low-complexity boundary (1 is most stringent). Ignored if not masking low-complexity sequences.
+* ``pct_id``: the percent identity threshold for filtering mapped reads.
+* ``frac``: the minimum fraction of the read that must be mapped to the reference to be kept.
 * ``host_fp``: the path to the folder with host/contaminant genomes (ending in
   *.fasta)
 
diff --git a/src/sunbeamlib/tibanna_profile.yaml b/src/sunbeamlib/tibanna_profile.yaml
deleted file mode 100755
index d70ccd39..00000000
--- a/src/sunbeamlib/tibanna_profile.yaml
+++ /dev/null
@@ -1,85 +0,0 @@
-# Default options for running sunbeam on slurm
-rerun-incomplete: True
-rerun-triggers: "mtime"
-latency-wait: 90
-jobs: 10
-keep-going: True
-notemp: True
-printshellcmds: True
-nolock: True
-verbose: True
-use-conda: True
-cores: 24
-tibanna: True
-default-remote-prefix: ""
-
-
-# Default resource configuration
-default-resources:
-  - runtime=15
-  - mem_mb=8000
-  - disk_mb=1000
-# set-threads: map rule names to threads
-set-threads:
-  - diamond_reads=8
-  - gene_hits=8
-  - adapter_removal_unpaired=4
-  - adapter_removal_paired=4
-  - trimmomatic_unpaired=4
-  - trimmomatic_paired=4
-  - align_to_host=4
-  - kraken2_classify_report=8
-  - megahit_paired=4
-  - megahit_unpaired=4
-  - run_blastn=4
-  - run_diamond_blastp=4
-  - run_diamond_blastx=4
-  - align_to_genome=4
-  # - samtools_convert=4
-# set-resources: map rule names to resources in general
-set-resources:
-  - fq_2_fa:mem_mb=8000
-  - fq_2_fa:runtime=60
-  - build_gene_clusters_diamond_db:mem_mb=32000
-  - build_gene_clusters_diamond_db:runtime=30
-  - diamond_reads:mem_mb=32000
-  - diamond_reads:runtime=1440
-  - gene_hits:mem_mb=32000
-  - gene_hits:runtime=1440
-  - sample_intake:mem_mb=4000
-  - sample_intake:runtime=20
-  - adapter_removal_paired:mem_mb=8000
-  - adapter_removal_paired:runtime=60
-  - qc_final:mem_mb=8000
-  - qc_final:runtime=120
-  - demultiplex:mem_mb=10000
-  - demultiplex:runtime=720
-  - trimmomatic_paired:mem_mb=8000
-  - trimmomatic_paired:runtime=240
-  - fastqc:mem_mb=4000
-  - fastqc:runtime=120
-  - remove_low_complexity:mem_mb=32000
-  - remove_low_complexity:runtime=120
-  - align_to_host:mem_mb=16000
-  - align_to_host:runtime=240
-  - filter_unmapped_reads:mem_mb=24000
-  - filter_unmapped_reads:runtime=240
-  - megahit_paired:mem_mb=20000
-  - megahit_paired:runtime=720
-  - final_filter:mem_mb=4000
-  - kraken2_classify_report:mem_mb=48000
-  - kraken2_classify_report:runtime=2880
-  - kraken2_biom:mem_mb=4000
-  - kraken2_biom:runtime=240
-  - classic_k2_biom:mem_mb=4000
-  - classic_k2_biom:runtime=240
-  - run_blastn:mem_mb=16000
-  - run_blastn:runtime=720
-  - run_diamond_blastp:mem_mb=16000
-  - run_diamond_blastp:runtime=720
-  - run_diamond_blastx:mem_mb=24000
-  - run_diamond_blastx:runtime=720
-  - prodigal:mem_mb=16000
-  - prodigal:runtime=720
-  - aggregate_results:mem_mb=8000
-  - aggregate_results:runtime=120
\ No newline at end of file

From 7dcd157ba3758f850249229162dc482d14926dfb Mon Sep 17 00:00:00 2001
From: ctbus <ctbushman@gmail.com>
Date: Fri, 13 Oct 2023 13:12:12 -0400
Subject: [PATCH 3/7] Update environments

---
 .github/PULL_REQUEST_TEMPLATE.md          |  2 +-
 environment.yml                           |  2 +-
 workflow/envs/cutadapt.linux-64.pin.txt   | 23 +++++-----
 workflow/envs/cutadapt.yml                |  3 +-
 workflow/envs/komplexity.linux-64.pin.txt | 31 ++++++-------
 workflow/envs/komplexity.yml              |  4 +-
 workflow/envs/qc.linux-64.pin.txt         | 32 +++++++-------
 workflow/envs/qc.yml                      |  4 +-
 workflow/envs/reports.linux-64.pin.txt    | 54 ++++++++++++-----------
 workflow/envs/reports.yml                 | 14 +++---
 10 files changed, 85 insertions(+), 84 deletions(-)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 6b838981..e9a807f9 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -5,6 +5,6 @@
 
 If this is for a release:
 * [ ] I have updated documentation
-* [ ] I have updated all conda pin files (`snakedeploy update-conda-envs workflow/envs/*.yml`)
+* [ ] I have updated all conda pin files (`snakedeploy pin-conda-envs workflow/envs/*.yml`)
 * [ ] I have updated the hardcoded version at the top of `install.sh` to match what this release's version will be
 * [ ] I have created a release archive that will be attached to this release
\ No newline at end of file
diff --git a/environment.yml b/environment.yml
index e3346ba9..f6824e76 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,4 +4,4 @@ channels:
 dependencies:
   - snakemake
   - git # Ensure sunbeam extend works even with tar installation of main pipeline
-  - python>=3.10
+  - python =3.12.0
diff --git a/workflow/envs/cutadapt.linux-64.pin.txt b/workflow/envs/cutadapt.linux-64.pin.txt
index 69a19d38..bafef845 100644
--- a/workflow/envs/cutadapt.linux-64.pin.txt
+++ b/workflow/envs/cutadapt.linux-64.pin.txt
@@ -5,26 +5,25 @@
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2
 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.1.0-hfd8a6a1_0.conda#067bcc23164642f4c226da631f2a2e1d
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.1.0-he5830b7_0.conda#56ca14d57ac29a75d23a39eb3ee0ddeb
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.1.0-he5830b7_0.conda#cd93f779ff018dd85c7544c015c9db3c
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
-https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-hd590300_1.conda#854e3e1623b39777140f199c5f9ab952
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-hcb278e6_0.conda#681105bccc2a3f7f1a837d47d39c9179
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.2-hd590300_0.conda#e5ac5227582d6c83ccf247288c0eb095
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.3-hd590300_0.conda#7bb88ce04c8deb9f7d763ae04a1da72f
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
-https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.42.0-h2797004_0.conda#fdaae20a1cf7cd62130a0973190a31b7
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.43.2-h2797004_0.conda#4b441a1ee22397d5a27dc1126b849edd
+https://conda.anaconda.org/conda-forge/linux-64/pigz-2.8-h2797004_0.conda#1832561770273ca7cf52b989dd83e6c3
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
-https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8c42eb62e9fc961af70bdd6a26e168
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/pigz-2.6-h27826a3_0.tar.bz2#677798489006b14291e8617223e34348
-https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.42.0-h2c6b66d_0.conda#1192f6ec654a5bc4ee1d64bdc4a3e5cc
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-h2797004_0.conda#513336054f884f95d9fd925748f41ef3
+https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.43.2-h2c6b66d_0.conda#c37b95bcd6c6833dacfd5df0ae2f4303
 https://conda.anaconda.org/conda-forge/linux-64/python-3.7.12-hf930737_100_cpython.tar.bz2#416558a6f46b7a1fa8db7d0e98aff56a
 https://conda.anaconda.org/conda-forge/noarch/bz2file-0.98-py_0.tar.bz2#784154d757e590f1f26c2427207bfe7a
-https://conda.anaconda.org/conda-forge/noarch/setuptools-68.0.0-pyhd8ed1ab_0.conda#5a7739d0f57ee64133c9d32e6507c46d
-https://conda.anaconda.org/conda-forge/noarch/wheel-0.41.1-pyhd8ed1ab_0.conda#8f467ba2db2b5470d297953d9c1f9c7d
+https://conda.anaconda.org/conda-forge/noarch/setuptools-68.2.2-pyhd8ed1ab_0.conda#fc2166155db840c634a1291a5c35a709
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.41.2-pyhd8ed1ab_0.conda#1ccd092478b3e0ee10d7a891adbf8a4f
 https://conda.anaconda.org/conda-forge/noarch/pip-23.2.1-pyhd8ed1ab_0.conda#e2783aa3f9235225eec92f9081c5b801
 https://conda.anaconda.org/bioconda/noarch/xopen-0.7.3-py_0.tar.bz2#ab0a57604100736fb19c421c0c0828c1
 https://conda.anaconda.org/bioconda/linux-64/dnaio-0.3-py37h14c3975_1.tar.bz2#d58d26d5cac1482ffbb60c91a31a9222
diff --git a/workflow/envs/cutadapt.yml b/workflow/envs/cutadapt.yml
index 2058827b..83e7fdbd 100755
--- a/workflow/envs/cutadapt.yml
+++ b/workflow/envs/cutadapt.yml
@@ -1,7 +1,6 @@
 channels:
-  - conda-forge
   - bioconda
 dependencies:
   - cutadapt
-  - python =3.10.12
+  #- python =3.12.0
 name: cutadapt
diff --git a/workflow/envs/komplexity.linux-64.pin.txt b/workflow/envs/komplexity.linux-64.pin.txt
index 24e22347..a79df973 100644
--- a/workflow/envs/komplexity.linux-64.pin.txt
+++ b/workflow/envs/komplexity.linux-64.pin.txt
@@ -4,24 +4,25 @@
 @EXPLICIT
 https://conda.anaconda.org/eclarke/linux-64/komplexity-0.3.6-musl.tar.bz2#991933bd25d6344b08011f622a1187c8
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2
 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2023b-h71feb2d_0.conda#6c80c63151d7f493dab457a0ba6c2523
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2#cedcee7c064c01c403f962c9e8d3c373
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda#939e3e74d8be4dac89ce83b20de2492a
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2#e4c94f80aef025c17ab0828cd85ef535
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda#6305a3dd2752c76335295da4e581f2fd
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
-https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206
-https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h7f98852_1000.tar.bz2#772d69f030955d9646d3d0eaf21d859d
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz2#f3f9de449d32ca9b9c66a22863c96f41
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2#4acfc691e64342b9dae57cf2adc63238
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.0-h0b41bf4_0.conda#2d833be81a21128e317325a01326d36f
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-hd590300_1.conda#854e3e1623b39777140f199c5f9ab952
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-hcb278e6_0.conda#681105bccc2a3f7f1a837d47d39c9179
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.3-hd590300_0.conda#7bb88ce04c8deb9f7d763ae04a1da72f
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
-https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar.bz2#2e5f9a37d487e1019fd4d8113adb2f9f
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.43.2-h2797004_0.conda#4b441a1ee22397d5a27dc1126b849edd
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
-https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8c42eb62e9fc961af70bdd6a26e168
-https://conda.anaconda.org/conda-forge/linux-64/python-3.11.0-he550d4f_1_cpython.conda#8d14fc2aa12db370a443753c8230be1e
-https://conda.anaconda.org/conda-forge/noarch/setuptools-67.6.0-pyhd8ed1ab_0.conda#e18ed61c37145bb9b48d1d98801960f7
-https://conda.anaconda.org/conda-forge/noarch/wheel-0.40.0-pyhd8ed1ab_0.conda#49bb0d9e60ce1db25e151780331bb5f3
-https://conda.anaconda.org/conda-forge/noarch/pip-23.0.1-pyhd8ed1ab_0.conda#8025ca83b8ba5430b640b83917c2a6f7
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-h2797004_0.conda#513336054f884f95d9fd925748f41ef3
+https://conda.anaconda.org/conda-forge/linux-64/python-3.12.0-hab00c5b_0_cpython.conda#7f97faab5bebcc2580f4f299285323da
+https://conda.anaconda.org/conda-forge/noarch/setuptools-68.2.2-pyhd8ed1ab_0.conda#fc2166155db840c634a1291a5c35a709
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.41.2-pyhd8ed1ab_0.conda#1ccd092478b3e0ee10d7a891adbf8a4f
+https://conda.anaconda.org/conda-forge/noarch/pip-23.2.1-pyhd8ed1ab_0.conda#e2783aa3f9235225eec92f9081c5b801
diff --git a/workflow/envs/komplexity.yml b/workflow/envs/komplexity.yml
index 1c0faae6..b0a85058 100755
--- a/workflow/envs/komplexity.yml
+++ b/workflow/envs/komplexity.yml
@@ -1,7 +1,7 @@
-name: komplexity
 channels:
   - eclarke
   - conda-forge
 dependencies:
   - komplexity
-  - python>=3.10
+  - python =3.12.0
+name: komplexity
diff --git a/workflow/envs/qc.linux-64.pin.txt b/workflow/envs/qc.linux-64.pin.txt
index 81e7d65e..0aa043fd 100644
--- a/workflow/envs/qc.linux-64.pin.txt
+++ b/workflow/envs/qc.linux-64.pin.txt
@@ -9,13 +9,13 @@ https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed3
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-hab24e00_0.tar.bz2#19410c3df09dfb12d1206132a1d357c5
 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.1.0-hfd8a6a1_0.conda#067bcc23164642f4c226da631f2a2e1d
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
 https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda#939e3e74d8be4dac89ce83b20de2492a
 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.1.0-he5830b7_0.conda#56ca14d57ac29a75d23a39eb3ee0ddeb
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.1.0-he5830b7_0.conda#cd93f779ff018dd85c7544c015c9db3c
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
 https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.7.2-h166bdaf_0.tar.bz2#4a826cd983be6c8fff07a64b6d2079e7
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
 https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2#14947d8770185e5153fdd04d4673ed37
@@ -27,13 +27,13 @@ https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz
 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda#6305a3dd2752c76335295da4e581f2fd
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
 https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-h166bdaf_0.tar.bz2#b62b52da46c39ee2bc3c162ac7f1804d
-https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-hd590300_1.conda#854e3e1623b39777140f199c5f9ab952
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
-https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.1-hd590300_0.conda#82bf6f63eb15ef719b556b63feec3a77
+https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.2-hd590300_0.conda#30de3fd9b3b602f7473f30e684eeea8c
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-hcb278e6_0.conda#681105bccc2a3f7f1a837d47d39c9179
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.2-hd590300_0.conda#e5ac5227582d6c83ccf247288c0eb095
-https://conda.anaconda.org/conda-forge/linux-64/pixman-0.40.0-h36c2ea0_0.tar.bz2#660e72c82f2e75a6b3fe6a6e75c79f19
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.3-hd590300_0.conda#7bb88ce04c8deb9f7d763ae04a1da72f
+https://conda.anaconda.org/conda-forge/linux-64/pixman-0.42.2-h59595ed_0.conda#700edd63ccd5fc66b70b1c028cea9a68
 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036
 https://conda.anaconda.org/conda-forge/linux-64/xorg-inputproto-2.3.2-h7f98852_1002.tar.bz2#bcd1b3396ec6960cbc1d2855a9e60b2b
 https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2#4b230e8381279d76131116660f5a241a
@@ -48,28 +48,28 @@ https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161
 https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-hcb278e6_1.conda#8b9b5aca60558d02ddaa09d599e55920
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
 https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.39-h753d276_0.conda#e1c890aebdebbfbf87e2c917187b4416
-https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.42.0-h2797004_0.conda#fdaae20a1cf7cd62130a0973190a31b7
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.43.2-h2797004_0.conda#4b441a1ee22397d5a27dc1126b849edd
 https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.13-h7f98852_1004.tar.bz2#b3653fdc58d03face9724f602218a904
 https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.40-hc3806b6_0.tar.bz2#69e2c796349cd9b273890bee0febfe1b
 https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-4_hd590300_perl5.conda#3e785bff761095eb7f8676f4694bd1b1
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
-https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8c42eb62e9fc961af70bdd6a26e168
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-h2797004_0.conda#513336054f884f95d9fd925748f41ef3
 https://conda.anaconda.org/conda-forge/linux-64/xorg-fixesproto-5.0-h7f98852_1002.tar.bz2#65ad6e1eb4aed2b0611855aff05e04f6
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.4-h7391055_0.conda#93ee23f12bc2e684548181256edd2cf6
 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.2-hfc55251_7.conda#32ae18eb2a687912fc9e92a501c0a11b
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
 https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.17-he4a0461_11.tar.bz2#23832bbbdfb4a2c05e2df120068b1c78
-https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-hca18f0e_1.conda#e1232042de76d24539a436d37597eb06
-https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.1-h659d440_0.conda#1b5126ec25763eb17ef74c8763d26e84
-https://conda.anaconda.org/conda-forge/linux-64/libglib-2.76.4-hebfc3b9_0.conda#c6f951789c888f7bbd2dd6858eab69de
+https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb
+https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
+https://conda.anaconda.org/conda-forge/linux-64/libglib-2.78.0-hebfc3b9_0.conda#e618003da3547216310088478e475945
 https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.2.0-hf544144_3.tar.bz2#53798351da909e181243e17dccee41ad
-https://conda.anaconda.org/conda-forge/linux-64/python-3.11.4-hab00c5b_0_cpython.conda#1c628861a2a126b9fc9363ca1b7d014e
+https://conda.anaconda.org/conda-forge/linux-64/python-3.12.0-hab00c5b_0_cpython.conda#7f97faab5bebcc2580f4f299285323da
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.4-h0b41bf4_0.conda#ea8fbfeb976ac49cbeb594e985393514
 https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda#0f69b688f52ff6da70bccb7ff7001d1d
 https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.12-hddcbb42_0.tar.bz2#797117394a4aa588de6d741b06fad80f
 https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-h4637d8d_4.conda#d4529f4dff3057982a7617c7ac58fde3
-https://conda.anaconda.org/conda-forge/noarch/setuptools-68.0.0-pyhd8ed1ab_0.conda#5a7739d0f57ee64133c9d32e6507c46d
-https://conda.anaconda.org/conda-forge/noarch/wheel-0.41.1-pyhd8ed1ab_0.conda#8f467ba2db2b5470d297953d9c1f9c7d
+https://conda.anaconda.org/conda-forge/noarch/setuptools-68.2.2-pyhd8ed1ab_0.conda#fc2166155db840c634a1291a5c35a709
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.41.2-pyhd8ed1ab_0.conda#1ccd092478b3e0ee10d7a891adbf8a4f
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h0b41bf4_2.conda#82b6df12252e6f32402b96dacc656fec
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxfixes-5.0.3-h7f98852_1004.tar.bz2#e9a21aa4d5e3e5f1aed71e8cefd46b6a
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.10-h7f98852_1003.tar.bz2#f59c1242cc1dd93e72c2ee2b360979eb
diff --git a/workflow/envs/qc.yml b/workflow/envs/qc.yml
index a47f0781..2ef188eb 100755
--- a/workflow/envs/qc.yml
+++ b/workflow/envs/qc.yml
@@ -1,4 +1,3 @@
-name: qc
 channels:
   - bioconda
   - conda-forge
@@ -6,4 +5,5 @@ dependencies:
   - bwa
   - fastqc
   - trimmomatic
-  - python =3.11.5
\ No newline at end of file
+  - python =3.12.0
+name: qc
diff --git a/workflow/envs/reports.linux-64.pin.txt b/workflow/envs/reports.linux-64.pin.txt
index a79d76d3..1538757e 100644
--- a/workflow/envs/reports.linux-64.pin.txt
+++ b/workflow/envs/reports.linux-64.pin.txt
@@ -3,37 +3,39 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2
 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-12.2.0-h337968e_19.tar.bz2#164b4b1acaedc47ee7e658ae6b308ca3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2#1030b1f38c129f2634eae026f704fe60
-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.11-3_cp311.conda#c2e2630ddb68cf52eec74dc7dfab20b5
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2023b-h71feb2d_0.conda#6c80c63151d7f493dab457a0ba6c2523
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-12.2.0-h69a702a_19.tar.bz2#cd7a806282c16e1f2d39a7e80d3a3e0d
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2#cedcee7c064c01c403f962c9e8d3c373
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda#939e3e74d8be4dac89ce83b20de2492a
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2#e4c94f80aef025c17ab0828cd85ef535
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda#6305a3dd2752c76335295da4e581f2fd
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
-https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206
-https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.21-pthreads_h78a6416_3.tar.bz2#8c5963a49b6035c40646a763293fbb35
-https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h7f98852_1000.tar.bz2#772d69f030955d9646d3d0eaf21d859d
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz2#f3f9de449d32ca9b9c66a22863c96f41
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2#4acfc691e64342b9dae57cf2adc63238
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.0-h0b41bf4_0.conda#2d833be81a21128e317325a01326d36f
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_2.conda#78fdab09d9138851dde2b5fe2a11019e
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-hd590300_1.conda#854e3e1623b39777140f199c5f9ab952
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-hcb278e6_0.conda#681105bccc2a3f7f1a837d47d39c9179
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.3-hd590300_0.conda#7bb88ce04c8deb9f7d763ae04a1da72f
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
-https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-16_linux64_openblas.tar.bz2#d9b7a8639171f6c6fa0a983edabcfe2b
-https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar.bz2#2e5f9a37d487e1019fd4d8113adb2f9f
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_2.conda#e75a75a6eaf6f318dae2631158c46575
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.43.2-h2797004_0.conda#4b441a1ee22397d5a27dc1126b849edd
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
-https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8c42eb62e9fc961af70bdd6a26e168
-https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-16_linux64_openblas.tar.bz2#20bae26d0a1db73f758fc3754cab4719
-https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-16_linux64_openblas.tar.bz2#955d993f41f9354bf753d29864ea20ad
-https://conda.anaconda.org/conda-forge/linux-64/python-3.11.0-he550d4f_1_cpython.conda#8d14fc2aa12db370a443753c8230be1e
-https://conda.anaconda.org/conda-forge/linux-64/numpy-1.24.2-py311h8e6699e_0.conda#90db8cc0dfa20853329bfc6642f887aa
-https://conda.anaconda.org/conda-forge/noarch/pytz-2023.2-pyhd8ed1ab_0.conda#d74d285d6628e55752df22fc84910279
-https://conda.anaconda.org/conda-forge/noarch/setuptools-67.6.0-pyhd8ed1ab_0.conda#e18ed61c37145bb9b48d1d98801960f7
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-h2797004_0.conda#513336054f884f95d9fd925748f41ef3
+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.24-pthreads_h413a1c8_0.conda#6e4ef6ca28655124dcde9bd500e44c32
+https://conda.anaconda.org/conda-forge/linux-64/python-3.12.0-hab00c5b_0_cpython.conda#7f97faab5bebcc2580f4f299285323da
+https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-18_linux64_openblas.conda#bcddbb497582ece559465b9cd11042e7
+https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2023.3-pyhd8ed1ab_0.conda#2590495f608a63625e165915fb4e2e34
+https://conda.anaconda.org/conda-forge/noarch/pytz-2023.3.post1-pyhd8ed1ab_0.conda#c93346b446cd08c169d843ae5fc0da97
+https://conda.anaconda.org/conda-forge/noarch/setuptools-68.2.2-pyhd8ed1ab_0.conda#fc2166155db840c634a1291a5c35a709
 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2
-https://conda.anaconda.org/conda-forge/noarch/wheel-0.40.0-pyhd8ed1ab_0.conda#49bb0d9e60ce1db25e151780331bb5f3
-https://conda.anaconda.org/conda-forge/noarch/pip-23.0.1-pyhd8ed1ab_0.conda#8025ca83b8ba5430b640b83917c2a6f7
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.41.2-pyhd8ed1ab_0.conda#1ccd092478b3e0ee10d7a891adbf8a4f
+https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-18_linux64_openblas.conda#93dd9ab275ad888ed8113953769af78c
+https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-18_linux64_openblas.conda#a1244707531e5b143c420c70573c8ec5
+https://conda.anaconda.org/conda-forge/noarch/pip-23.2.1-pyhd8ed1ab_0.conda#e2783aa3f9235225eec92f9081c5b801
 https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.8.2-pyhd8ed1ab_0.tar.bz2#dd999d1cc9f79e67dbb855c8924c7984
-https://conda.anaconda.org/conda-forge/linux-64/pandas-1.5.3-py311h2872171_0.conda#a129a2aa7f5c2f45808399d60c3080f2
+https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.0-py312heda63a1_0.conda#9b4f35e4d83e2a8b17868b65beb438d9
+https://conda.anaconda.org/conda-forge/linux-64/pandas-2.1.1-py312hfb8ada1_1.conda#77ebdc18c9a54c929a332d59965f197f
diff --git a/workflow/envs/reports.yml b/workflow/envs/reports.yml
index 42e0d02a..128f2f5d 100755
--- a/workflow/envs/reports.yml
+++ b/workflow/envs/reports.yml
@@ -1,7 +1,7 @@
-name: reports
-channels:
-  - conda-forge
-dependencies:
-  - numpy
-  - pandas
-  - python>=3.10
\ No newline at end of file
+channels:
+  - conda-forge
+dependencies:
+  - numpy
+  - pandas
+  - python =3.12.0
+name: reports

From b64aabfe52abcb82a74ca5b8d0ce2a97969957ec Mon Sep 17 00:00:00 2001
From: ctbus <ctbushman@gmail.com>
Date: Fri, 13 Oct 2023 22:16:46 -0400
Subject: [PATCH 4/7] Add test tar release workflow

---
 .github/PULL_REQUEST_TEMPLATE.md       |  2 +-
 .github/workflows/test_tar_release.yml | 34 ++++++++++++++++++++++++++
 dev_scripts/generate_archive.sh        |  2 +-
 docs/quickstart.rst                    |  4 +--
 docs/usage.rst                         |  4 +--
 5 files changed, 40 insertions(+), 6 deletions(-)
 create mode 100755 .github/workflows/test_tar_release.yml

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index e9a807f9..fdcc27a2 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -7,4 +7,4 @@ If this is for a release:
 * [ ] I have updated documentation
 * [ ] I have updated all conda pin files (`snakedeploy pin-conda-envs workflow/envs/*.yml`)
 * [ ] I have updated the hardcoded version at the top of `install.sh` to match what this release's version will be
-* [ ] I have created a release archive that will be attached to this release
\ No newline at end of file
+* [ ] I have created a release archive that will be attached to this release (`bash dev_scripts/generate_archive.sh`)
\ No newline at end of file
diff --git a/.github/workflows/test_tar_release.yml b/.github/workflows/test_tar_release.yml
new file mode 100755
index 00000000..6599b065
--- /dev/null
+++ b/.github/workflows/test_tar_release.yml
@@ -0,0 +1,34 @@
+name: Test Tarball on Release
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    
+
+jobs:
+  test-tarball:
+    name: Test Tarball
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: setup-conda
+        uses: s-weigand/setup-conda@v1.2.1
+        with:
+          # Additional channels like 'conda-forge' which can be used to install packages
+          conda-channels: '' # optional, default is 
+
+      - name: Download and Extract
+        shell: bash
+        run: |
+          wget https://github.com/sunbeam-labs/sunbeam/releases/latest/download/sunbeam.tar.gz
+          mkdir sunbeam
+          tar -zxf sunbeam.tar.gz -C sunbeam
+          cd sunbeam && ./install.sh -e sunbeam
+      
+      - name: Run Tests
+        shell: bash
+        run: |
+          conda activate sunbeam
+          cd sunbeam
+          pytest -vvl tests/
\ No newline at end of file
diff --git a/dev_scripts/generate_archive.sh b/dev_scripts/generate_archive.sh
index 92d17255..50991370 100644
--- a/dev_scripts/generate_archive.sh
+++ b/dev_scripts/generate_archive.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 # $1 is the version for this release (e.g. 4.0.0 or 4.1.3-rc.2)
 
-tar -czvf sunbeam$1.tar.gz etc/ extensions/.placeholder sunbeamlib/ tests/ workflow/ environment.yml install.sh Readme.md setup.py MANIFEST.in pytest.ini
\ No newline at end of file
+tar -czv --exclude '__pycache__' -f sunbeam$1.tar.gz etc/ extensions/.placeholder src/sunbeamlib/ stable_env/ tests/ workflow/ environment.yml install.sh README.md pyproject.toml MANIFEST.in pytest.ini
\ No newline at end of file
diff --git a/docs/quickstart.rst b/docs/quickstart.rst
index 7fbc5387..fe87a13a 100644
--- a/docs/quickstart.rst
+++ b/docs/quickstart.rst
@@ -18,9 +18,9 @@ There are two installation methods available, installing via git or via tar. We
 
       .. code-block:: shell
 
-         wget https://github.com/sunbeam-labs/sunbeam/releases/download/v4.0.0/sunbeam.tar.gz
+         wget https://github.com/sunbeam-labs/sunbeam/releases/latest/download/sunbeam.tar.gz
          mkdir sunbeam4.0.0
-         tar -zxf sunbeam4.0.0.tar.gz -C sunbeam4.0.0
+         tar -zxf sunbeam.tar.gz -C sunbeam4.0.0
          cd sunbeam4.0.0 && ./install.sh
 
    .. tab:: git install
diff --git a/docs/usage.rst b/docs/usage.rst
index b44e7a9a..8379cfa2 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -31,9 +31,9 @@ versions you want)).
 
       .. code-block:: shell
 
-         wget https://github.com/sunbeam-labs/sunbeam/releases/download/v4.0.0/sunbeam.tar.gz
+         wget https://github.com/sunbeam-labs/sunbeam/releases/latest/download/sunbeam.tar.gz
          mkdir sunbeam4.0.0
-         tar -zxf sunbeam4.0.0.tar.gz -C sunbeam4.0.0
+         tar -zxf sunbeam.tar.gz -C sunbeam4.0.0
          cd sunbeam4.0.0 && ./install.sh
 
    .. tab:: git install

From e27c176163fd3882c0ed146c72e8ab62ddd67296 Mon Sep 17 00:00:00 2001
From: ctbus <ctbushman@gmail.com>
Date: Fri, 13 Oct 2023 22:17:59 -0400
Subject: [PATCH 5/7] Trigger on PR

---
 .github/workflows/test_tar_release.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test_tar_release.yml b/.github/workflows/test_tar_release.yml
index 6599b065..75944936 100755
--- a/.github/workflows/test_tar_release.yml
+++ b/.github/workflows/test_tar_release.yml
@@ -3,7 +3,8 @@ name: Test Tarball on Release
 on:
   release:
     types: [published]
-  workflow_dispatch:
+  pull_request:
+    branches: [ main, master ]
     
 
 jobs:

From 427e2c492aa2bedf9d3a75b3b79bbbfe879244d8 Mon Sep 17 00:00:00 2001
From: ctbus <ctbushman@gmail.com>
Date: Fri, 13 Oct 2023 22:25:12 -0400
Subject: [PATCH 6/7] Conda being weird

---
 .github/workflows/test_tar_release.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test_tar_release.yml b/.github/workflows/test_tar_release.yml
index 75944936..2e4d1fee 100755
--- a/.github/workflows/test_tar_release.yml
+++ b/.github/workflows/test_tar_release.yml
@@ -25,11 +25,11 @@ jobs:
           wget https://github.com/sunbeam-labs/sunbeam/releases/latest/download/sunbeam.tar.gz
           mkdir sunbeam
           tar -zxf sunbeam.tar.gz -C sunbeam
-          cd sunbeam && ./install.sh -e sunbeam
+          cd sunbeam && ./install.sh -e sunbeam -m
       
       - name: Run Tests
         shell: bash
         run: |
-          conda activate sunbeam
+          source activate sunbeam
           cd sunbeam
           pytest -vvl tests/
\ No newline at end of file

From f1e929cb4746ad7598183014c2f6247464bcd72c Mon Sep 17 00:00:00 2001
From: ctbus <ctbushman@gmail.com>
Date: Fri, 13 Oct 2023 22:41:25 -0400
Subject: [PATCH 7/7] Finalize tar test workflow

---
 .github/workflows/test_tar_release.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/test_tar_release.yml b/.github/workflows/test_tar_release.yml
index 2e4d1fee..c23ed4d7 100755
--- a/.github/workflows/test_tar_release.yml
+++ b/.github/workflows/test_tar_release.yml
@@ -3,8 +3,6 @@ name: Test Tarball on Release
 on:
   release:
     types: [published]
-  pull_request:
-    branches: [ main, master ]
     
 
 jobs:
@@ -25,7 +23,7 @@ jobs:
           wget https://github.com/sunbeam-labs/sunbeam/releases/latest/download/sunbeam.tar.gz
           mkdir sunbeam
           tar -zxf sunbeam.tar.gz -C sunbeam
-          cd sunbeam && ./install.sh -e sunbeam -m
+          cd sunbeam && ./install.sh -e sunbeam
       
       - name: Run Tests
         shell: bash