rcsb · piehld · Nov 4, 2025 · Nov 4, 2025 · Nov 4, 2025 · Nov 12, 2025
diff --git a/HISTORY.txt b/HISTORY.txt
@@ -145,3 +145,5 @@
 04-May-2025 - V1.32 Add methods and support for IHM structure loading
 12-Jun-2025 - V1.33 Add transformation to populate rcsb_entry_container_identifiers.pubmed_id and rcsb_polymer_entity_container_identifiers.uniprot_ids
 27-Jun-2025 - V1.34 Add transformation to populate rcsb_polymer_instance_info
+ 4-Nov-2025 - V1.35 Strip newline characters from 'chem_comp.name';
+                    Switch to 'pyproject.toml' file and hatch build system, and update pipelines to Python 3.13
diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/README.md b/README.md
@@ -24,14 +24,9 @@ git clone --recurse-submodules https://github.com/rcsb/py-rcsb_utils_dictionary.
 ```
 
 Optionally, run test suite (Python versions 3.7+) using
-[setuptools](https://setuptools.readthedocs.io/en/latest/) or
 [tox](http://tox.readthedocs.io/en/latest/example/platform.html):
 
 ```bash
-python setup.py test
-
-or simply run
-
 tox
 ```
 

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -12,7 +12,6 @@ name: $(BuildDefinitionName)_$(Date:yyyyMMdd)$(Rev:.rr)
 
 trigger:
   - master
-  - utilsdict-*
 
 pr:
   - master
@@ -27,20 +26,18 @@ schedules:
 
 jobs:
   - template: azure-template-tox-job.yml
-    parameters: { tox: "format_pep8", python: "3.10", os: "linux" }
+    parameters: { tox: "format_pep8", python: "3.13", os: "linux" }
   - template: azure-template-tox-job.yml
-    parameters: { tox: "lint_pylint", python: "3.10", os: "linux" }
+    parameters: { tox: "lint_pylint", python: "3.13", os: "linux" }
   - template: azure-template-tox-job.yml
-    parameters: { tox: "test_coverage", python: "3.10", os: "linux" }
+    parameters: { tox: "test_coverage", python: "3.13", os: "linux" }
     #
   - template: azure-template-tox-job.yml
-    parameters: { tox: "py310", python: "3.10", os: "linux" }
+    parameters: { tox: "py313", python: "3.13", os: "linux" }
   #
   - template: azure-template-tox-job.yml
-    parameters: { tox: "py310", python: "3.10", os: "macos" }
+    parameters: { tox: "py313", python: "3.13", os: "macos" }
   #
-  #- template: azure-template-publish-job.yml
-  #  parameters: {tox: "py310", python: "3.10", os: 'macos'}
   - template: azure-template-publish-job.yml
-    parameters: { tox: "py310", python: "3.10", os: "linux" }
+    parameters: { tox: "py313", python: "3.13", os: "linux" }
   #
diff --git a/azure-template-publish-job.yml b/azure-template-publish-job.yml
@@ -41,7 +41,7 @@ jobs:
     - script: ls -lR $(Pipeline.Workspace)/${{ format('sw_{0}_{1}', parameters.tox, parameters.os) }}
       displayName: "Listing of downloaded artifacts"
     #
-    - script: python -m pip install --upgrade pip twine setuptools wheel
+    - script: python -m pip install --upgrade pip twine wheel hatch
       displayName: 'Install packaging tools'
     #
     - task: DownloadSecureFile@1

diff --git a/azure-template-tox-job.yml b/azure-template-tox-job.yml
@@ -35,6 +35,7 @@ jobs:
       #
       - checkout: self
         submodules: true
+        fetchDepth: 1
       #
       - ${{ if startsWith(parameters.os, 'macos') }}:
           - bash: |
@@ -66,62 +67,96 @@ jobs:
           #
           - script: sudo apt-get update
             displayName: "update apt"
-          #- script: sudo apt-get upgrade
-          #  displayName: 'upgrade apt'
-          #- script: sudo apt-get update
-          #  displayName: 'update apt'
           - script: sudo apt-get install flex
             displayName: "Install flex"
           - script: sudo apt-get install bison
             displayName: "Install bison"
       #
+      - ? ${{ if and(contains(parameters.fixtures, 'mysql'), startsWith(parameters.os, 'linux')) }}
+        : - bash: |
+              sudo apt-get install libmysqlclient-dev python-mysqldb
+              sudo apt list --installed | grep -i mysql
+            displayName: "Install mysql development libraries"
+          - bash: |
+              echo "Retarting mysql service"
+              sudo systemctl restart mysql.service
+              mysql -V
+              mysql --user=root --password=root -e "use mysql; select * from user;"
+              #
+              echo "Try resetting password"
+              mysqladmin --user=root --password=root password 'ChangeMeSoon'
+              #
+              # mysql -u root  -p root -e "SET PASSWORD FOR root@'localhost' = PASSWORD(‘ChangeMeSoon’);"
+              # mysql -u root  -p root -e "FLUSH PRIVILEGES; update mysql.user set password=password('ChangeMeSoon') where user='root'; FLUSH PRIVILEGES;"
+              # UPDATE mysql.user SET Password=PASSWORD('ChangeMeSoon') WHERE User='root';
+
+              echo "Running preliminary mysql setup"
+              mysql --user=root --password=ChangeMeSoon <<_EOF_
+                DELETE FROM mysql.user WHERE User='';
+                DELETE FROM mysql.user WHERE User='root' AND Host NOT IN ('localhost', '127.0.0.1', '::1');
+                DROP DATABASE IF EXISTS test;
+                DELETE FROM mysql.db WHERE Db='test' OR Db='test\\_%';
+                FLUSH PRIVILEGES;
+              _EOF_
+              ps -ef | grep -i my
+              mysql --user=root --password=ChangeMeSoon -e "show databases;"
+              #
+            displayName: "Start and configure mysql ..."
+
+        # -----
+      - ? ${{ if and(contains(parameters.fixtures, 'mongodb'), startsWith(parameters.os, 'linux')) }}
+        : # Mongo install
+          - script: |
+              sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 9DA31620334BD75D9DCB49F368818C72E52529D4
+              sudo apt list --installed | grep mongodb
+              echo "deb [ arch=amd64,arm64 ] https://repo.mongodb.org/apt/ubuntu xenial/mongodb-org/4.0 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-4.0.list
+              sudo apt-get update
+              sudo apt-get install -y mongodb-org
+              sudo apt list --installed | grep mongo
+            displayName: "Installing mongodb"
+          #
+          - script: |
+              sudo service mongod start
+              sudo ss -tulpn
+            displayName: "Start Mongo service"
+        #
+      #
       - script: 'python -c "import sys; print(sys.version); print(sys.executable)"'
         displayName: show python information
       #
       - script: python -m pip install --upgrade pip tox
         displayName: "Install tools"
         #
-      - script: pip install -r requirements.txt
+      - script: pip install .[tests]
         displayName: "Install dependencies"
       #
+      # - task: DownloadSecureFile@1
+      #   name: oelicense
+      #   displayName: 'Download OE license file'
+      #   inputs:
+      #     secureFile: 'oe_license.txt'
       #
-      - task: DownloadSecureFile@1
-        name: oelicense
-        displayName: "Download OE license file"
-        inputs:
-          secureFile: "oe_license.txt"
-
       - ${{ if startsWith(parameters.tox, 'py') }}:
           - script: |
-              export OE_LICENSE=$(oelicense.secureFilePath)
               export CONFIG_SUPPORT_TOKEN_ENV=$(VAR_CONFIG_SUPPORT_TOKEN_ENV)
               ${{ format('python -m tox -e {0}', parameters.tox) }}
             displayName: "Running tox task"
-      - ? ${{ if and(not(startsWith(parameters.tox, 'py')), startsWith(parameters.python, '3.10')) }}
+      - ? ${{ if and(not(startsWith(parameters.tox, 'py')), startsWith(parameters.python, '3.13')) }}
         : - script: |
-              export OE_LICENSE=$(oelicense.secureFilePath)
               export CONFIG_SUPPORT_TOKEN_ENV=$(VAR_CONFIG_SUPPORT_TOKEN_ENV)
-              ${{ format('python -m tox -e {0}-py310', parameters.tox) }}
-            displayName: "Running tox task"
-      - ? ${{ if and(not(startsWith(parameters.tox, 'py')), startsWith(parameters.python, '3.9')) }}
-        : - script: |
-              export OE_LICENSE=$(oelicense.secureFilePath)
-              export CONFIG_SUPPORT_TOKEN_ENV=$(VAR_CONFIG_SUPPORT_TOKEN_ENV)
-              ${{ format('python -m tox -e {0}-py39', parameters.tox) }}
+              ${{ format('python -m tox -e {0}-py313', parameters.tox) }}
             displayName: "Running tox task"
       #
       #  Build artifacts if this is a test target (i.e. labeled as py##)
       #
       - ${{ if startsWith(parameters.tox, 'py') }}:
-          - script: pip install --upgrade pip twine setuptools wheel
+          - script: pip install --upgrade pip build twine hatch
             displayName: "Acquire build tools"
-          - script: python setup.py  sdist --dist-dir "$(System.DefaultWorkingDirectory)/dist"
-            displayName: "Build source dist"
-          - script: python setup.py  bdist_wheel --dist-dir "$(System.DefaultWorkingDirectory)/dist"
-            displayName: "Build wheel"
-          #
-          - script: python setup.py  sdist --dist-dir "$(System.DefaultWorkingDirectory)/udist"
-            displayName: "Build source dist"
+          - script: python -m build --sdist --wheel --outdir "$(System.DefaultWorkingDirectory)/dist"
+            displayName: "Build source and wheel distributions"
+          - script: python -m build --sdist --outdir "$(System.DefaultWorkingDirectory)/udist"
+            displayName: "Build source distribution to udist"
+
           #
           # Check the install artifacts
           - script: ls -lR "$(System.DefaultWorkingDirectory)/dist" "$(System.DefaultWorkingDirectory)/udist"

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,88 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "rcsb.utils.dictionary"
+description = "RCSB Python Dictionary Utility Classes"
+readme = "README.md"
+authors = [
+    { name="John Westbrook", email="john.westbrook@rcsb.org" }
+]
+maintainers = [
+    { name="Dennis Piehl", email="dennis.piehl@rcsb.org" }
+]
+license = "Apache-2.0"
+license-files = ["LICENSE"]
+requires-python = ">=3.9"
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Developers",
+    "Natural Language :: English",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.13",
+]
+dependencies = [
+    "scipy",
+    "numpy",
+    "mmcif >= 0.91.0",
+    "rcsb.utils.chemref >= 0.91",
+    "rcsb.utils.citation >= 0.25",
+    "rcsb.utils.config >= 0.40",
+    "rcsb.utils.ec >= 0.25",
+    "rcsb.utils.io >= 1.52",
+    "rcsb.utils.multiproc >= 0.19",
+    "rcsb.utils.repository >= 0.50",
+    "rcsb.utils.seq >= 0.82",
+    "rcsb.utils.struct >= 0.47",
+    "rcsb.utils.targets >= 0.88",
+    "rcsb.utils.taxonomy >= 0.43",
+    "rcsb.utils.validation >= 0.31",
+    "rcsb.utils.insilico3d >= 0.42",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+tests = ["tox", "pylint", "black>=21.5b1", "flake8", "coverage"]
+
+[project.urls]
+Homepage = "https://github.com/rcsb/py-rcsb_utils_dictionary"
+
+# ----------------  hatch configuration ----------------
+[tool.hatch.version]
+path = "rcsb/utils/dictionary/__init__.py"
+
+[tool.hatch.build]
+exclude = [
+    "/rcsb/utils/test*/**",
+    "/rcsb/mock-*/**",
+    "test*/**"
+]
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "/rcsb/**",
+    "/README.md",
+    "/LICENSE",
+    "/HISTORY.txt",
+    "/pyproject.toml"
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["rcsb"]
+
+[tool.hatch.envs.default]
+skip-install = true
+
+# ----------------  test configuration ----------------
+[tool.hatch.envs.hatch-test]
+dependencies = ["tox"]
+
+[tool.hatch.envs.hatch-test.scripts]
+run = ["tox"]
+
+# ----------------  UV configuration ----------------
+# Add this to prevent uv from automatically creating venvs within individual packages when running 'uv run ...' from within the package directory
+[tool.uv]
+managed = false
diff --git a/rcsb/utils/dictionary/DictMethodChemRefHelper.py b/rcsb/utils/dictionary/DictMethodChemRefHelper.py
@@ -10,6 +10,7 @@
 #   18-Sep-2023 dwp Load COD references separately from CCDC/CSD references
 #    3-May-2024 dwp Change BIRD citation method to copy categories instead of just renaming, and only apply to BIRD entries
 #   25-Jul-2024 dwp Fix assignment logic of Pharos data for rcsb_chem_comp_related.related_mapping_method in addChemCompRelated()
+#    4-Nov-2025 dwp Strip newline characters from 'chem_comp.name'
 ##
 """
 Helper class implements external method references supporting chemical
@@ -901,6 +902,8 @@ def addChemCompSynonyms(self, dataContainer, catName, **kwargs):
             ccObj = dataContainer.getObj("chem_comp")
             ccId = ccObj.getValue("id", 0)
             ccName = ccObj.getValue("name", 0)
+            if ccName:
+                ccName = ccName.replace("\n", "")  # strip newline characters
             # ccSynonymL = []
             # if ccObj.hasAttribute("pdbx_synonyms"):
             #    ccSynonymL = str(ccObj.getValue("pdbx_synonyms", 0)).split(";")

diff --git a/rcsb/utils/dictionary/DictMethodCompModelHelper.py b/rcsb/utils/dictionary/DictMethodCompModelHelper.py
@@ -381,7 +381,7 @@ def buildCompModelProvenance(self, dataContainer, catName, **kwargs):
                 return False
 
             if catName != "rcsb_comp_model_provenance":
-                logger.warning("input catName (%s) not 'rcsb_comp_model_provenance'")
+                logger.warning("input catName (%s) not 'rcsb_comp_model_provenance'", catName)
 
             catName = "rcsb_comp_model_provenance"