pdb_fixer clean up

PolusAI · May 21, 2024 · debd679 · debd679
1 parent 5965ec4
commit debd679
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Showing 18 changed files with 9 additions and 5 deletions.
diff --git a/utils/pdbfixer-plugin/.bumpversion.cfg → ...re-changes/pdbfixer-tool/.bumpversion.cfg b/utils/pdbfixer-plugin/.bumpversion.cfg → ...re-changes/pdbfixer-tool/.bumpversion.cfg
diff --git a/utils/pdbfixer-plugin/.dockerignore → ...cture-changes/pdbfixer-tool/.dockerignore b/utils/pdbfixer-plugin/.dockerignore → ...cture-changes/pdbfixer-tool/.dockerignore
diff --git a/utils/pdbfixer-plugin/.gitignore → ...tructure-changes/pdbfixer-tool/.gitignore b/utils/pdbfixer-plugin/.gitignore → ...tructure-changes/pdbfixer-tool/.gitignore
diff --git a/utils/pdbfixer-plugin/CHANGELOG.md → ...ucture-changes/pdbfixer-tool/CHANGELOG.md b/utils/pdbfixer-plugin/CHANGELOG.md → ...ucture-changes/pdbfixer-tool/CHANGELOG.md
diff --git a/utils/pdbfixer-plugin/Dockerfile → ...tructure-changes/pdbfixer-tool/Dockerfile b/utils/pdbfixer-plugin/Dockerfile → ...tructure-changes/pdbfixer-tool/Dockerfile
@@ -1,4 +1,4 @@
-# docker build -f Dockerfile -t mrbrandonwalker/pdbfixer .
+# docker build -f Dockerfile -t polusai/pdbfixer-tool:0.1.0 .
 
 FROM condaforge/mambaforge
 # pdbfixer not installable with poetry

diff --git a/utils/pdbfixer-plugin/README.md → ...structure-changes/pdbfixer-tool/README.md b/utils/pdbfixer-plugin/README.md → ...structure-changes/pdbfixer-tool/README.md
diff --git a/utils/pdbfixer-plugin/VERSION → ...s/structure-changes/pdbfixer-tool/VERSION b/utils/pdbfixer-plugin/VERSION → ...s/structure-changes/pdbfixer-tool/VERSION
diff --git a/utils/pre-process/structure-changes/pdbfixer-tool/build-docker.sh b/utils/pre-process/structure-changes/pdbfixer-tool/build-docker.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/pdbfixer-tool:${version}
diff --git a/utils/pdbfixer-plugin/environment.yml → ...ure-changes/pdbfixer-tool/environment.yml b/utils/pdbfixer-plugin/environment.yml → ...ure-changes/pdbfixer-tool/environment.yml
diff --git a/utils/pdbfixer-plugin/ict.yml → ...s/structure-changes/pdbfixer-tool/ict.yml b/utils/pdbfixer-plugin/ict.yml → ...s/structure-changes/pdbfixer-tool/ict.yml
@@ -1,7 +1,7 @@
 specVersion: 0.1.0
 name: labshare/pdbfixer
 version: 0.1.0
-container: polusai/pdbfixer-plugin:0.1.0
+container: polusai/pdbfixer-tool:0.1.0
 entrypoint: ""
 title: pdbfixer
 description: Fix pdbfiles.

diff --git a/utils/pdbfixer-plugin/pdb_fixer.cwl → ...changes/pdbfixer-tool/pdb_fixer_0.1.0.cwl b/utils/pdbfixer-plugin/pdb_fixer.cwl → ...changes/pdbfixer-tool/pdb_fixer_0.1.0.cwl
@@ -12,7 +12,7 @@ baseCommand: ["python", "-m", "polus.mm.utils.pdbfixer"]
 
 hints:
   DockerRequirement:
-    dockerPull: mrbrandonwalker/pdbfixer
+    dockerPull: polusai/pdbfixer-tool@sha256:a44142a9b23b60950bdc2cb7d6c760f4216cc7f59dad0468f92ff87a976f3ab2
 
 inputs:
   input_pdb_path:

diff --git a/utils/pdbfixer-plugin/pyproject.toml → ...ture-changes/pdbfixer-tool/pyproject.toml b/utils/pdbfixer-plugin/pyproject.toml → ...ture-changes/pdbfixer-tool/pyproject.toml
diff --git a/...n/src/polus/mm/utils/pdbfixer/__init__.py → ...l/src/polus/mm/utils/pdbfixer/__init__.py b/...n/src/polus/mm/utils/pdbfixer/__init__.py → ...l/src/polus/mm/utils/pdbfixer/__init__.py
diff --git a/...n/src/polus/mm/utils/pdbfixer/__main__.py → ...l/src/polus/mm/utils/pdbfixer/__main__.py b/...n/src/polus/mm/utils/pdbfixer/__main__.py → ...l/src/polus/mm/utils/pdbfixer/__main__.py
diff --git a/...n/src/polus/mm/utils/pdbfixer/pdbfixer.py → ...l/src/polus/mm/utils/pdbfixer/pdbfixer.py b/...n/src/polus/mm/utils/pdbfixer/pdbfixer.py → ...l/src/polus/mm/utils/pdbfixer/pdbfixer.py
diff --git a/utils/pdbfixer-plugin/tests/1msn_protein.pdb → ...nges/pdbfixer-tool/tests/1msn_protein.pdb b/utils/pdbfixer-plugin/tests/1msn_protein.pdb → ...nges/pdbfixer-tool/tests/1msn_protein.pdb
diff --git a/utils/pdbfixer-plugin/tests/__init__.py → ...e-changes/pdbfixer-tool/tests/__init__.py b/utils/pdbfixer-plugin/tests/__init__.py → ...e-changes/pdbfixer-tool/tests/__init__.py
diff --git a/utils/pdbfixer-plugin/tests/test_pdbfixer.py → ...nges/pdbfixer-tool/tests/test_pdbfixer.py b/utils/pdbfixer-plugin/tests/test_pdbfixer.py → ...nges/pdbfixer-tool/tests/test_pdbfixer.py
@@ -47,7 +47,7 @@ def test_pdbfixer() -> None:
 
 def test_cwl_pdb_fixer() -> None:
     """Test the pdbfixer function in cwltool."""
-    cwl_file = Path("pdb_fixer.cwl")
+    cwl_file = Path("pdb_fixer_0.1.0.cwl")
     input_to_props = parse_cwl_arguments(cwl_file)
     input_pdb_path = "1msn_protein.pdb"
     input_pdb_path = str(Path(__file__).resolve().parent / Path(input_pdb_path))
@@ -60,7 +60,7 @@ def test_cwl_pdb_fixer() -> None:
     input_to_props["input_helper_pdb_path"]["path"] = input_helper_pdb_path
     input_to_props["input_helper_pdb_path"]["class"] = "File"
     input_to_props["output_pdb_path"] = "output.pdb"
-    input_yaml_path = Path("pdb_fixer.yml")
+    input_yaml_path = Path("pdb_fixer_0.1.0.yml")
     create_input_yaml(input_to_props, input_yaml_path)
     stdout, stderr = call_cwltool(cwl_file, input_yaml_path)