From 10619d6e88fa7b36cb370cbcaca1b047ee35fb38 Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Mon, 5 Feb 2024 12:19:05 -0500
Subject: [PATCH 1/2] fix checkout command for docs building action

Seems like after using the default git checkout github actions step, we can't use other git commands because of some nonsense with the ssh key. Rather than deal with figuring that out, I have just moved all of the weirdness we were doing in the git command to the original checkout command.

I have also removed the `rm -rf build/html` command. That directory does not exist before the clone (I think this was carried over from a previous script, because it doesn't actually break anything).
---
 .github/workflows/docs.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index d9a60ec946..3139afe15e 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -16,6 +16,9 @@ jobs:
         shell: bash -l {0}
     steps:
       - uses: actions/checkout@v2
+        with:
+          ref: gh-pages
+          path: build/html
       - name: Setup Mambaforge Python 3.7
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -58,8 +61,6 @@ jobs:
           git config user.name github-actions
           git config user.email github-actions@github.com
           cd documentation
-          rm -rf build/html
-          git clone --single-branch --branch gh-pages --origin official git@github.com:ReactionMechanismGenerator/RMG-Py.git build/html
           make html
       - name: Check documentation links
         continue-on-error: true

From a5c74170c9249605d18c247d68fb5c86890cd0aa Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Mon, 5 Feb 2024 12:23:04 -0500
Subject: [PATCH 2/2] run checkout command twice, once per needed branch

this was originally cloning main and then gh-pages, restoring this behavior (but using the checkout step rather than manually git calls) since the environment.yml file stored in main is needed for later steps
---
 .github/workflows/docs.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 3139afe15e..046b22fcdb 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -16,9 +16,6 @@ jobs:
         shell: bash -l {0}
     steps:
       - uses: actions/checkout@v2
-        with:
-          ref: gh-pages
-          path: build/html
       - name: Setup Mambaforge Python 3.7
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -46,6 +43,10 @@ jobs:
           cd RMG-Py
           sed -i '/embedsignature/s/# //g' setup.py
           make
+      - uses: actions/checkout@v2
+        with:
+          ref: gh-pages
+          path: build/html
       - name: Make documentation - for testing
         if: ${{  github.event_name != 'push' || github.repository != 'ReactionMechanismGenerator/RMG-Py' }}
         run: |