Adds Pixi task to update dependency version numbers

README.md

@@ -87,6 +87,12 @@ running the following command inside it.
 pixi run --frozen dev-setup
 ```
 Follow the prompts to configure the set-up to your liking.
+Among other configurations, this set-up clones the other Auto-Mech repositories
+into the parent directory of your mechdriver repository.
+```
+ls ..
+autochem  autofile  autoio  mechanalyzer  mechdriver
+```
 If you run into issues, see [Appendix C](#appendix-c-manual-developer-setup) for
 manual set-up instructions.
 
@@ -107,6 +113,22 @@ For more information on activating Pixi environments, see
 You can then run any of the examples [in the `examples/` directory](./examples/)
 as [described above](#run).
 
+### Git Helper Tasks
+
+The following Pixi tasks are available to facilitate Git operations with your
+five local Auto-Mech repositories:
+
+1. `pixi run pull`. This does a `git pull --rebase upstream dev` on all five
+repositories to update them against the central Auto-Mech upstream.
+2. `pixi run git <commands>`. This runs whatever `git` commands you pass it in
+all five repositories.
+
+For example, a common operation you might wish to do is:
+```
+pixi run pull                   # Rebase each repo against upstream
+pixi run git push origin dev    # Push each repo to origin
+```
+
 ### Test
 
 > [!TIP]
@@ -178,7 +200,7 @@ override the commit hash check on GitHub Actions and allow your tests to pass.
 
 > [!WARNING]
 > Versions are now automatically handled by the BumpVer versioning tool.
-> Therefore, do not manually change the version of a given package in its
+> Therefore, **do not** manually change the version of a given package in its
 > `pyproject.toml`.  Instead, the version will be automatically updated by
 > triggering the release workflow as described below.
 
@@ -195,22 +217,23 @@ This will (1.) bump the version number, (2.) publish the conda package to the
 [`auto-mech` channel](https://anaconda.org/Auto-Mech/), and (3.) create an
 associated GitHub release.
 
-For now, if you have updated the conda package for a lower-level module such as
-`autoio` and want these changes to take effect in MechDriver, you will also need
-to update the following two tables in the MechDriver `pyproject.toml`.
+If you have done this for one or more of the lower-level repositories, you will
+also need to update the MechDriver `pyproject.toml` file with their new version
+numbers.
+You can do so as follows:
 ```
-[tool.pixi.package.run-dependencies]
-...
-autoio = "==<new version number>"
-
-[tool.pixi.dependencies]
-...
-autoio = "==<new version number>"
+pixi run pull   # Pull the release commits from upstream
+pixi run update # Update the version numbers in pyproject.toml
 ```
-These two dependency tables **must match exactly** to ensure that the packaged
-version of the code matches the tested version.
+This will update the `package.run-dependencies` and `dependencies` tables in
+your `pyproject.toml` with the new version numbers of the lower-level
+repositories and update the lockfile.
+If you make any manual changes to these tables,
+**make sure that they match exactly**.
+This is necessary to ensure that the packaged version of the code matches the
+tested version.
 
-## Subtask Parallelization
+## Experimental Feature: Subtask Parallelization
 
 As an experimental feature in MechDriver, you can parallelize across subtasks in
 your workflow with

pyproject.toml

@@ -133,7 +133,7 @@ dev-setup-hq = { cmd = "./scripts/dev-setup-hq.sh", cwd = "." }
 dev-setup-config = { cmd = "./scripts/dev-setup-config.sh", cwd = "." }
 dev-setup = { depends-on = ["dev-setup-repos", "dev-setup-hq", "dev-setup-config"] }
 git = { cmd = "./scripts/git.sh", cwd = "." }
-update = { cmd = "./scripts/update.sh", cwd = "." }
+pull = { cmd = "./scripts/pull.sh", cwd = "." }
 
 [tool.pixi.feature.test.tasks]
 test = { cmd = "./scripts/test.py" }
@@ -145,6 +145,7 @@ dev-test = { cmd = "./scripts/test.py" }
 [tool.pixi.feature.build.tasks]
 upload = "rattler-build upload anaconda -o Auto-Mech *.conda"
 current-version = "bumpver show -n | awk -F': ' '/Current Version: / {print $2}'"
+update = { cmd = "./scripts/update.sh", cwd = "." }
 
 [tool.bumpver]
 current_version = "0.2025.0"

scripts/pull.sh

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+
+# This script updates each repo against a remote
+# (It also updates the amech-dev repo.)
+#
+# Performs a pull --rebase
+#
+# Arguments:
+#   - Remote to update against (default: upstream)
+#   - Branch to update (default: dev)
+
+set -e  # if any command fails, quit
+REPOS=("autochem" "autoio" "autofile" "mechanalyzer" "mechdriver")
+
+# 0. Read arguments
+REMOTE=${1:-upstream}
+BRANCH=${2:-dev}
+
+echo "The following commands will be run in each repository:"
+echo "    git checkout ${BRANCH}"
+echo "    git pull --rebase ${REMOTE} ${BRANCH}"
+read -p "Is this what you want to do? [y/n] " yn
+
+if [[ $yn =~ ^[Yy]$ ]]; then
+    # 1. Navigate to mechdriver parent directory
+    (
+        cd ..
+
+        # 2. Loop through each repo and update
+        for repo in ${REPOS[@]}
+        do
+            printf "\n*** Updating in $(realpath ${repo}) ***\n"
+            (
+                cd ${repo} && \
+                git checkout ${BRANCH} && \
+                git pull --rebase ${REMOTE} ${BRANCH}
+            )
+            printf "******\n"
+        done
+    )
+fi

scripts/update.sh

@@ -10,32 +10,16 @@
 #   - Branch to update (default: dev)
 
 set -e  # if any command fails, quit
-REPOS=("autochem" "autoio" "autofile" "mechanalyzer" "mechdriver")
+REPOS=("autochem" "autoio" "autofile" "mechanalyzer")
 
-# 0. Read arguments
-REMOTE=${1:-upstream}
-BRANCH=${2:-dev}
+# 1. Loop through each repo and update
+for repo in ${REPOS[@]}
+do
+    version=$(pixi run --manifest-path ../$repo current-version)
+    echo Setting $repo version to $version
+    sed -i -E "s/($repo *= *\"==)[0-9]+\.[0-9]+\.[0-9]+(\" *)/\1${version}\2/" pyproject.toml
+done
 
-echo "The following commands will be run in each repository:"
-echo "    git checkout ${BRANCH}"
-echo "    git pull --rebase ${REMOTE} ${BRANCH}"
-read -p "Is this what you want to do? [y/n] " yn
-
-if [[ $yn =~ ^[Yy]$ ]]; then
-    # 1. Navigate to mechdriver parent directory
-    (
-        cd ..
-
-        # 2. Loop through each repo and update
-        for repo in ${REPOS[@]}
-        do
-            printf "\n*** Updating in $(realpath ${repo}) ***\n"
-            (
-                cd ${repo} && \
-                git checkout ${BRANCH} && \
-                git pull --rebase ${REMOTE} ${BRANCH}
-            )
-            printf "******\n"
-        done
-    )
-fi
+# 2. Update lockfile
+echo Updating lockfile
+pixi lock