From 552fbfd86345f1e144c6409be29d558f64313962 Mon Sep 17 00:00:00 2001 From: jonwzheng Date: Mon, 13 Jan 2025 13:36:19 -0500 Subject: [PATCH 1/4] attempt to update CI to use artifacts v4 for upload --- .github/workflows/CI.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 4e2cc7a77d..3404fd956a 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -357,14 +357,14 @@ jobs: - name: Upload regression summary artifact # the annotate workflow uses this artifact to add a comment to the PR - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 if : ${{ github.event_name == 'pull_request' }} with: name: regression_summary path: summary.txt - name: Upload Comparison Results - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: regression_test_comparison_results path: | From bd33f203b6f7b95b75353a7a4c449ca8f1e4cbb3 Mon Sep 17 00:00:00 2001 From: jonwzheng Date: Wed, 15 Jan 2025 14:32:55 -0500 Subject: [PATCH 2/4] use conda-forge for graphviz to avoid bug see issue #2750. rmg channel for graphviz can lead to errors on some configurations, which was previously causing CI/run failures --- environment.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index da15b2dfe3..e0dc8095ae 100644 --- a/environment.yml +++ b/environment.yml @@ -32,13 +32,14 @@ dependencies: - xlrd - xlwt - h5py - - graphviz - markupsafe - psutil # conda-forge not default, since default has a version information bug # (see https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2421) - conda-forge::ncurses - conda-forge::suitesparse + # see https://github.com/ReactionMechanismGenerator/RMG-Py/issues/2750 + - conda-forge::graphviz # external software tools for chemistry - coolprop From 806b875880435f54bee4833a51615f17eaf57317 Mon Sep 17 00:00:00 2001 From: jonwzheng Date: Fri, 17 Jan 2025 13:15:44 -0500 Subject: [PATCH 3/4] fix conda environment typo --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index e0dc8095ae..2b9c4bd551 100644 --- a/environment.yml +++ b/environment.yml @@ -39,7 +39,7 @@ dependencies: - conda-forge::ncurses - conda-forge::suitesparse # see https://github.com/ReactionMechanismGenerator/RMG-Py/issues/2750 - - conda-forge::graphviz + - conda-forge::graphviz # external software tools for chemistry - coolprop From 1c7babe7623a66fc19d2d454f9d270f80803de6a Mon Sep 17 00:00:00 2001 From: jonwzheng Date: Fri, 17 Jan 2025 13:16:19 -0500 Subject: [PATCH 4/4] add symlink to libtiff5 from libtiff6 in build runner to avoid runner bug --- .github/workflows/docs.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index ef3509d78f..d722f595a2 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -36,6 +36,11 @@ jobs: activate-environment: rmg_env use-mamba: true + - name: Make libtiff Symlink to Avoid Runner Bug + run: | # This action may need to be removed/adjusted in future runs. + if [ ! -f /usr/lib/x86_64-linux-gnu/libtiff.so.5 ] && [ -f /usr/lib/x86_64-linux-gnu/libtiff.so.6 ]; then sudo ln -s /usr/lib/x86_64-linux-gnu/libtiff.so.6 /usr/lib/x86_64-linux-gnu/libtiff.so.5; fi + find /usr/lib -name libtiff* + - name: Install sphinx run: mamba install -y sphinx