update to neutcurve 1.0 and snakemake 8.0 (#19)

* update `snakemake` to 8.0 and `neutcurve` to 1.0 * re-run pipeline * lint directly with `ruff` rather than via `nbqa`
jbloomlab · Dec 26, 2023 · 3babd8a · 3babd8a
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diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -28,16 +28,12 @@ jobs:
           auto-update-conda: true
           channel-priority: strict
 
-      - name: lint code with ruff
+      - name: lint with ruff
         # NOTE: must specify the shell so that conda init updates bashrc see:
         #      https://github.com/conda-incubator/setup-miniconda#IMPORTANT
         shell: bash -el {0}
         run: ruff check .
 
-      - name: lint Jupyter notebooks with ruff
-        shell: bash -el {0}
-        run: nbqa ruff .
-
       - name: check code format with black
         shell: bash -el {0}
         run: black --check .

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # CHANGELOG
 
+### version 1.1.0
+- Update software environment to include `neutcurve` 1.0 and `snakemake` 8.0.
+- Fix linting of notebooks with `ruff`
+
 ## version 1.0.0
 The initial version of this pipeline was created from prior code from Andrea Loes and Will Hannon.
 The pipeline was re-factored into this initial version with the following design goals:

diff --git a/README.md b/README.md
@@ -53,12 +53,14 @@ This creates a file called `gitmodules` and the `seqneut-pipeline` submodule, wh
 If at some point you want to updated the version of the pipeline, simply `cd` into the `seqneut-pipeline` subdirectory and pull or checkout the version you want.
 
 To use the pipeline, you then need to add a few things to your main-level repo.
-The first is a top-level `Snakefile` that includes `seqneut-pipeline`, reads in your configuration, file, and contains as some of its targets the outputs of `seqneut-pipeline`.
+The first is a top-level `Snakefile` that includes your configuration, `seqneut-pipeline`, and outputs of `seqneut-pipeline` as targets of the `all` rule.
 So minimally that top-level `Snakefile` should contain the following lines (it can also contain additional stuff if you also have it running project-specific analyses on the output of the pipeline):
 ```
+import os
+
 configfile: "config.yml"
 
-include: "seqneut-pipeline/seqneut-pipeline.smk"
+include: os.path.join(config["seqneut-pipeline"], "seqneut-pipeline.smk")
 
 rule all:
     input:
@@ -78,7 +80,7 @@ Finally, you need to create a `conda` environment that minimally includes the pa
 You can either create your own environment containing these, or simply build and use the one specified in [environment.yml](environment.yml) file of `seqneut-pipeline`, which is named `seqneut-pipeline`. So if you are using that environment, you can simply run the pipeline with:
 ```
 conda activate seqneut-pipeline
-snakemake -j <n_jobs> --use-conda --keep-going
+snakemake -j <n_jobs> --software-deployment-method conda --keep-going
 ```
 
 The use of `--keep-going` is recommended for the QC steps below as it will create the notebooks helpful for manually doing the QC.

diff --git a/docs/process_counts_plate11.html b/docs/process_counts_plate11.html
diff --git a/docs/process_counts_plate2.html b/docs/process_counts_plate2.html
diff --git a/docs/serum_titers_M099d0.html b/docs/serum_titers_M099d0.html
diff --git a/docs/serum_titers_M099d30.html b/docs/serum_titers_M099d30.html
diff --git a/docs/serum_titers_Y044d30.html b/docs/serum_titers_Y044d30.html
diff --git a/docs/serum_titers_Y154d182.html b/docs/serum_titers_Y154d182.html
diff --git a/docs/titers.html b/docs/titers.html
diff --git a/environment.yml b/environment.yml
@@ -6,20 +6,19 @@ channels:
   - defaults
 
 dependencies:
-  - altair=5.1.2
+  - altair=5.2
   - black-jupyter
   - jupyterlab
   - mamba
   - markdown=3.5
-  - nbqa
   - pandas=2.1
   - papermill=2.4
   - pip
   - python=3.11
   - ruamel.yaml=0.18.5
   - snakefmt
-  - snakemake=7.32
+  - snakemake=8.0.1
   - ruff
   - pip:
     - dms_variants==1.4.3
-    - neutcurve==0.10.1
+    - neutcurve==1.0.0
diff --git a/ruff.toml b/ruff.toml
@@ -4,3 +4,5 @@ builtins = [
     "snakemake",  # may appear undefined as passed to scripts via `Snakefile`
     "display",  # builtin of Jupyter notebooks
 ]
+
+extend-include = ["*.ipynb"]
diff --git a/seqneut-pipeline.smk b/seqneut-pipeline.smk
@@ -8,7 +8,7 @@ Designed to be included in another ``Snakefile`` that specifies the config.
 import pandas as pd
 
 
-snakemake.utils.min_version("7.32")
+snakemake.utils.min_version("8.0")
 
 
 include: "funcs.smk"  # include functions

diff --git a/test_example/results/aggregated_titers/titers.csv b/test_example/results/aggregated_titers/titers.csv
@@ -1,145 +1,145 @@
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+Y154d182,A/Bangladesh/8036/2021,208.6,3,14,interpolated
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 Y154d182,A/Belgium/H0038/2022,3018,3,340.4,interpolated
 Y154d182,A/Brisbane/02/2018,3786,4,443.6,interpolated
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+Y154d182,A/Brisbane/48/2022,198.4,3,4.122,interpolated
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 Y154d182,A/Chester/5355/2022,201.6,3,7.105,interpolated
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 Y154d182,A/Ghana/138/2020,2794,3,294.1,interpolated
-Y154d182,A/Ghana/2080/2020,2762,3,665.7,interpolated
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 Y154d182,A/Hawaii/70/2019,3675,4,496.1,interpolated
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+Y154d182,A/India-PUN-NIV328484/2021,239.5,3,40.8,interpolated
+Y154d182,A/India-Pune-Nivcov2221170/2022,169.4,2,0.85,interpolated
+Y154d182,A/India/Pun-NIV312851/2021,219.3,3,77.32,interpolated
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 Y154d182,A/Michigan/45/2015,5578,4,1182,interpolated
 Y154d182,A/Newcastle/2/2022,215.6,3,40.11,interpolated
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 Y154d182,A/Nimes/871/2021,3441,3,568.7,interpolated
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-Y154d182,A/Paris/31196/2021,5608,3,1720,interpolated
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+Y154d182,A/Paris/31196/2021,5608,3,1714,interpolated
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 Y154d182,A/SouthAfrica/R16462/2021,3200,3,785.8,interpolated
-Y154d182,A/Sydney/43/2022,244,3,45.68,interpolated
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+Y154d182,A/Sydney/43/2022,227.5,3,47.18,interpolated
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 Y154d182,A/Togo/0304/2021,2602,3,631.4,interpolated
 Y154d182,A/Togo/845/2020,1815,3,265.8,interpolated
-Y154d182,A/Utah/27/2022,253.2,3,16.26,interpolated
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+Y154d182,A/Utah/27/2022,242.2,3,16.22,interpolated
+Y154d182,A/Washington/23/2020,620.7,3,17.23,interpolated
 Y154d182,A/Wisconsin/588/2019,1153,3,295.7,interpolated