From d7b450e5fa655c5c6ad71fe411c745e93ffd7aac Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Mon, 22 Jun 2026 16:50:22 -0700 Subject: [PATCH 1/4] Test kartograf 2.0 --- environment.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment.yaml b/environment.yaml index d7e7242..da8b30b 100644 --- a/environment.yaml +++ b/environment.yaml @@ -19,3 +19,4 @@ dependencies: - pip: - git+https://github.com/OpenFreeEnergy/openfe_analysis@main # Use conda-forge v0.5 after new openfe release updates pins on openfe-analysis - git+https://github.com/OpenFreeEnergy/cinnabar@main # Use conda-forge v0.6.0 after new openfe release updates pins on cinnabar + - git+https://github.com/OpenFreeEnergy/kartograf@main # Use conda-forge v2.0 after new openfe release updates pins on kartogra From 78fe52abef257169c162d74847203b0dcde6773d Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Mon, 22 Jun 2026 18:39:57 -0700 Subject: [PATCH 2/4] update location of MappingRMSDScorer --- networks/konnektor_kartograf_example.ipynb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/networks/konnektor_kartograf_example.ipynb b/networks/konnektor_kartograf_example.ipynb index 5f58f7f..ad914e5 100644 --- a/networks/konnektor_kartograf_example.ipynb +++ b/networks/konnektor_kartograf_example.ipynb @@ -71,7 +71,8 @@ "outputs": [], "source": [ "# Load AtomMapper and Scorer\n", - "from kartograf import KartografAtomMapper, MappingRMSDScorer\n", + "from kartograf import KartografAtomMapper\n", + "from kartograf.mapping_metrics import MappingRMSDScorer\n", "\n", "mapper = KartografAtomMapper()\n", "scorer = MappingRMSDScorer()" From 145c57e51f3a58e0db08fe5800b1f75eb52304a8 Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Tue, 23 Jun 2026 07:12:16 -0700 Subject: [PATCH 3/4] Pin versions for pip installs --- environment.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/environment.yaml b/environment.yaml index da8b30b..51d6690 100644 --- a/environment.yaml +++ b/environment.yaml @@ -17,6 +17,6 @@ dependencies: - openfe==1.11.0 - openff-interchange-base != 0.5.1 # https://github.com/openforcefield/openff-interchange/issues/1450 - pip: - - git+https://github.com/OpenFreeEnergy/openfe_analysis@main # Use conda-forge v0.5 after new openfe release updates pins on openfe-analysis - - git+https://github.com/OpenFreeEnergy/cinnabar@main # Use conda-forge v0.6.0 after new openfe release updates pins on cinnabar - - git+https://github.com/OpenFreeEnergy/kartograf@main # Use conda-forge v2.0 after new openfe release updates pins on kartogra + - git+https://github.com/OpenFreeEnergy/openfe_analysis@v0.5.0 # Use conda-forge v0.5 after new openfe release updates pins on openfe-analysis + - git+https://github.com/OpenFreeEnergy/cinnabar@v0.6.0 # Use conda-forge v0.6.0 after new openfe release updates pins on cinnabar + - git+https://github.com/OpenFreeEnergy/kartograf@v2.0.0 # Use conda-forge v2.0 after new openfe release updates pins on kartogra From de6af51af4d12572b137230f226d0b4c32ab37f3 Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Tue, 23 Jun 2026 07:17:27 -0700 Subject: [PATCH 4/4] cinnabun doesn't have a v in the tag --- environment.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yaml b/environment.yaml index 51d6690..99ee1dc 100644 --- a/environment.yaml +++ b/environment.yaml @@ -18,5 +18,5 @@ dependencies: - openff-interchange-base != 0.5.1 # https://github.com/openforcefield/openff-interchange/issues/1450 - pip: - git+https://github.com/OpenFreeEnergy/openfe_analysis@v0.5.0 # Use conda-forge v0.5 after new openfe release updates pins on openfe-analysis - - git+https://github.com/OpenFreeEnergy/cinnabar@v0.6.0 # Use conda-forge v0.6.0 after new openfe release updates pins on cinnabar + - git+https://github.com/OpenFreeEnergy/cinnabar@0.6.0 # Use conda-forge v0.6.0 after new openfe release updates pins on cinnabar - git+https://github.com/OpenFreeEnergy/kartograf@v2.0.0 # Use conda-forge v2.0 after new openfe release updates pins on kartogra