From 3ae97c76334d00b915c7d5563b6cffcbf3676c3c Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Mon, 1 Jul 2024 17:07:45 -0400 Subject: [PATCH 1/4] Add refresh-prog-info doc --- docs/source/index.rst | 1 + docs/source/refresh-prog-info.rst | 11 +++++++++++ 2 files changed, 12 insertions(+) create mode 100644 docs/source/refresh-prog-info.rst diff --git a/docs/source/index.rst b/docs/source/index.rst index 02bcc94..d005604 100644 --- a/docs/source/index.rst +++ b/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 diff --git a/docs/source/refresh-prog-info.rst b/docs/source/refresh-prog-info.rst new file mode 100644 index 0000000..639ab72 --- /dev/null +++ b/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``. From d923ec27694776fe26cc1e5867f17f0607d76353 Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Mon, 1 Jul 2024 17:08:48 -0400 Subject: [PATCH 2/4] update version in conf.py --- docs/source/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 23cdcfa..04c3e3b 100644 --- a/docs/source/conf.py +++ b/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' From 34d4fff158109b7cdce0210ea7b5604d8c19e9b7 Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Mon, 8 Jul 2024 15:17:47 -0400 Subject: [PATCH 3/4] update recommended piscem --- .github/workflows/sanitize-cargo.toml | 38 +++++++++++++++++++++++++++ Cargo.lock | 2 +- Cargo.toml | 2 +- src/utils/prog_utils.rs | 4 +-- 4 files changed, 42 insertions(+), 4 deletions(-) create mode 100644 .github/workflows/sanitize-cargo.toml diff --git a/.github/workflows/sanitize-cargo.toml b/.github/workflows/sanitize-cargo.toml new file mode 100644 index 0000000..6ae73e9 --- /dev/null +++ b/.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} diff --git a/Cargo.lock b/Cargo.lock index 46c3a3d..c0dd138 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -2385,7 +2385,7 @@ checksum = "f27f6278552951f1f2b8cf9da965d10969b2efdea95a6ec47987ab46edfe263a" [[package]] name = "simpleaf" -version = "0.17.0" +version = "0.17.1" dependencies = [ "anyhow", "chrono", diff --git a/Cargo.toml b/Cargo.toml index 17653c9..90c0e48 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "simpleaf" -version = "0.17.0" +version = "0.17.1" edition = "2021" authors = [ "Rob Patro ", diff --git a/src/utils/prog_utils.rs b/src/utils/prog_utils.rs index 4c6db6f..ae7f37d 100644 --- a/src/utils/prog_utils.rs +++ b/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(¤t_ver) { // nothing to do here From 47c5fe7900c4b42374a869fcb68d14503058c543 Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Mon, 8 Jul 2024 22:02:22 -0400 Subject: [PATCH 4/4] update env yaml --- simpleaf_conda_env.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/simpleaf_conda_env.yml b/simpleaf_conda_env.yml index 90142dd..0ef72b2 100644 --- a/simpleaf_conda_env.yml +++ b/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