Merge pull request #154 from COMBINE-lab/dev

merge dev into main

.github/workflows/sanitize-cargo.toml

@@ -0,0 +1,38 @@
+name: Sanitize Cargo
+on: 
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: write
+
+jobs:
+  sanitize_cargo_file:
+    if: "contains(github.event.head_commit.message, '[do_tag]')"
+    runs-on: ubuntu-latest
+    # This is optional; it exposes the plan to your job as an environment variable
+    #env:
+    #  PLAN: ${{ inputs.plan }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.PAT_TOK }}
+      - uses: dtolnay/rust-toolchain@stable
+      - name: Install cargo-sanitize
+        run: |
+          cargo install cargo-sanitize
+      - name: Sanitize Cargo.toml file
+        run: |
+          cp Cargo.toml Cargo.toml.cs_orig
+          cargo-sanitize -i Cargo.toml.cs_orig -o Cargo.toml
+      - name: Tag and push new commit
+        run: |
+          export VERSION_TAG=`cargo read-manifest | jq ".version" | tr -d '"'`
+          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git add Cargo.toml.cs_orig
+          git add Cargo.toml
+          git commit -m "create sanitized release"
+          git tag --force -a v${VERSION_TAG} -m "version ${VERSION_TAG}"
+          git push --force origin v${VERSION_TAG}

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "simpleaf"
-version = "0.17.0"
+version = "0.17.1"
 edition = "2021"
 authors = [
   "Rob Patro <[email protected]>",

docs/source/conf.py

@@ -22,7 +22,7 @@
 author = 'Dongze He, Rob Patro'
 
 # The full version, including alpha/beta/rc tags
-release = '0.15.0'
+release = '0.17.0'
 
 master_doc = 'index'
 

docs/source/index.rst

@@ -45,6 +45,7 @@ That's it for initial notes.  Use the menu below to learn more about the `simple
    inspect-command.rst
    index-command.rst
    quant-command.rst
+   refresh-prog-info.rst
    workflow.rst
    LICENSE.rst
 

docs/source/refresh-prog-info.rst

@@ -0,0 +1,11 @@
+``refresh-prog-info`` command
+=============================
+
+The ``refresh-prog-info`` command reads the paths stored for the executables used by ``simpleaf`` (specifically those for 
+``alevin-fry``, ``piscem`` and ``salmon``), and for each of the installed programs, fetches and updates the associated versions
+of the programs.
+
+This command is useful because ``simpleaf`` records the version associated with each of the registered tools when their paths are
+first set with the ``--set-paths`` command.  However, if he executable is subsequently updated, the associate version won't be 
+revised (since this operation may have been done outside of ``simpleaf``).  This command provides a simple way to ensure that the 
+proper version information is associated with each of the programs registered with ``simpleaf``.

simpleaf_conda_env.yml

@@ -9,4 +9,4 @@ dependencies:
   - libboost>=1.85.0
   - salmon>=1.10.3
   - alevin-fry>=0.8.2
-  - piscem>=0.9.0
+  - piscem>=0.10.0

src/utils/prog_utils.rs

@@ -172,9 +172,9 @@ pub struct ReqProgs {
 
 impl ReqProgs {
     pub fn issue_recommended_version_messages(&self) {
-        // Currently (07/01/2024) want to recommend piscem >= 0.9.0
+        // Currently (07/08/2024) want to recommend piscem >= 0.10.0
         if let Some(ref piscem_info) = self.piscem {
-            let desired_ver = VersionReq::parse(">=0.9.0").unwrap();
+            let desired_ver = VersionReq::parse(">=0.10.0").unwrap();
             let current_ver = Version::parse(&piscem_info.version).unwrap();
             if desired_ver.matches(&current_ver) {
                 // nothing to do here