From 284d86f38955122df10be993c9ff6a6aa07b14f0 Mon Sep 17 00:00:00 2001
From: Harriet Dashnow <h.dashnow@gmail.com>
Date: Mon, 9 Dec 2024 11:20:41 -0700
Subject: [PATCH 1/2] add short CI workflow (requires python only, no R)

---
 .github/workflows/update-loci.yaml | 55 ++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 .github/workflows/update-loci.yaml

diff --git a/.github/workflows/update-loci.yaml b/.github/workflows/update-loci.yaml
new file mode 100644
index 0000000..59bc23f
--- /dev/null
+++ b/.github/workflows/update-loci.yaml
@@ -0,0 +1,55 @@
+name: Update data
+
+on:
+  pull_request:
+    branches: main
+    paths:
+      - "data/**"
+      - "scripts/**"
+      - "workflow/**"
+      - ".github/workflows/**"
+  workflow_dispatch:
+
+jobs:
+  update:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+
+    steps:
+      - name: Debug dump
+        uses: crazy-max/ghaction-dump-context@v2
+
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Miniconda environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          activate-environment: strchive
+          environment-file: scripts/environment.yml
+          python-version: 3.12
+          auto-activate-base: false
+      - run: |
+          conda info
+
+      - name: Check loci and update bed files (short)
+        if: ${{ github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'}}
+        run: snakemake --config stages="skip-refs"
+
+      - name: Open pull request with updated files
+        if: ${{ !(github.event_name == 'pull_request') }}
+        uses: peter-evans/create-pull-request@v7
+        with:
+          branch: update-data
+          title: Update data
+
+      - name: Commit updated files to current pull request
+        if: ${{ github.event_name == 'pull_request' }}
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: Update data
\ No newline at end of file

From cb667c812a6fbdce3bce74c4206a36a11adc8246 Mon Sep 17 00:00:00 2001
From: hdashnow <hdashnow@users.noreply.github.com>
Date: Mon, 9 Dec 2024 19:40:32 +0000
Subject: [PATCH 2/2] Update data

---
 .../setup-miniconda-patched-environment.yml   | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 scripts/setup-miniconda-patched-environment.yml

diff --git a/scripts/setup-miniconda-patched-environment.yml b/scripts/setup-miniconda-patched-environment.yml
new file mode 100644
index 0000000..52c06b7
--- /dev/null
+++ b/scripts/setup-miniconda-patched-environment.yml
@@ -0,0 +1,23 @@
+name: strchive
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - pandas
+  - numpy
+  - biopython
+  - defopt
+  - snakemake
+  - jsbeautifier
+  - r-base
+  - r-essentials
+  - r-jsonlite
+  - r-dplyr
+  - r-rentrez
+  - r-easypubmed
+  - r-stringr
+  - r-purrr
+  - pip
+  - pip:
+      - manubot
+  - python=3.12