update rootstock default branch to main (#275)

merges #275

README.md

@@ -16,7 +16,7 @@ Package documentation is available at <https://manubot.github.io/manubot> (auto-
 The `manubot cite` command-line interface retrieves and formats bibliographic metadata for user-supplied persistent identifiers like DOIs or PubMed IDs.
 The `manubot process` command-line interface prepares scholarly manuscripts for Pandoc consumption.
 The `manubot process` command is used by Manubot manuscripts, which are based off the [Rootstock template](https://github.com/manubot/rootstock), to automate several aspects of manuscript generation.
-See Rootstock's [manuscript usage guide](https://github.com/manubot/rootstock/blob/master/USAGE.md) for more information.
+See Rootstock's [manuscript usage guide](https://github.com/manubot/rootstock/blob/main/USAGE.md) for more information.
 
 **Note:**
 If you want to experience Manubot by editing an existing manuscript, see <https://github.com/manubot/try-manubot>.
@@ -33,7 +33,7 @@ The Manubot version of this manuscript is available at <https://greenelab.github
 
 ## Installation
 
-If you are using the `manubot` Python package as part of a manuscript repository, installation of this package is handled though the Rootstock's [environment specification](https://github.com/manubot/rootstock/blob/master/build/environment.yml).
+If you are using the `manubot` Python package as part of a manuscript repository, installation of this package is handled though the Rootstock's [environment specification](https://github.com/manubot/rootstock/blob/main/build/environment.yml).
 For other use cases, this package can be installed via `pip`.
 
 Install the latest release version [from PyPI](https://pypi.org/project/manubot/):

manubot/process/metadata.py

@@ -182,13 +182,13 @@ def get_rootstock_commit() -> Optional[str]:
     """
     Return the most recent commit in common between the git repository
     this function is run within (usually a Manubot manuscript repository)
-    and the `master` branch of the `rootstock` remote.
+    and the `main` branch of the `rootstock` remote.
 
     WARNING: This function may modify the git repository its executed within:
 
     - if the repository has not set the `roostock` remote, it is set to
       point to the default Rootstock repository of <https://github.com/manubot/rootstock>.
-    - fetches the latest commits in the `master` branch of the `rootstock` remote
+    - fetches the latest commits in the `main` branch of the `rootstock` remote
     """
     from manubot.util import shlex_join
 
@@ -202,9 +202,9 @@ def get_rootstock_commit() -> Optional[str]:
         )
     # find most recent common ancestor commit
     try:
-        args = ["git", "fetch", "rootstock", "master"]
+        args = ["git", "fetch", "rootstock", "main"]
         subprocess.check_output(args, stderr=subprocess.PIPE, universal_newlines=True)
-        args = ["git", "merge-base", "HEAD", "rootstock/master"]
+        args = ["git", "merge-base", "HEAD", "rootstock/main"]
         output = subprocess.check_output(
             args, stderr=subprocess.PIPE, universal_newlines=True
         )

manubot/process/tests/manuscripts/citation-rendering/readme.md

@@ -16,8 +16,8 @@ pandoc \
   --csl=https://gist.githubusercontent.com/rmzelle/a3f1fab95a4b136962fce5b1b7cdeaf8/raw/0e2478d17476c633b080b5197e145d1e2b858a2f/manubot.csl \
   --metadata link-citations=true \
   --bibliography=content/manual-references.json \
-  --include-after-body=https://github.com/manubot/rootstock/raw/master/build/themes/default.html \
-  --include-after-body=https://github.com/manubot/rootstock/raw/master/build/plugins/tooltips.html \
+  --include-after-body=https://github.com/manubot/rootstock/raw/main/build/themes/default.html \
+  --include-after-body=https://github.com/manubot/rootstock/raw/main/build/plugins/tooltips.html \
   content/01.main-text.md
 ```