ci:drop:python:3.13::rdkit

[ci skip]

.devcontainer/Dockerfile

@@ -9,7 +9,9 @@ ENV https_proxy=http://a100-internal.yaoyy.moe:10089
 ENV all_proxy=http://a100-internal.yaoyy.moe:10089
 ENV GITHUB_ROSETTA_TEST=YES
 
-RUN apt-get update -y && apt-get install git curl wget -y
+RUN apt-get update -y && apt-get install git curl wget -y \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
 
 RUN python -m pip config set global.index-url https://mirrors.bfsu.edu.cn/pypi/web/simple \
     && python -m pip install --no-cache-dir --upgrade pip \

.github/workflows/CI.yml

@@ -19,7 +19,6 @@ jobs:
           - "3.10"
           - "3.11"
           - "3.12"
-          - "3.13"
 
     uses: YaoYinYing/action-python/.github/workflows/[email protected]
     with:

README.md

@@ -147,6 +147,8 @@ print(f"Full Path: {rosetta_binary.full_path}")
 ### Wrapping the Rosetta
 
 ```python
+# Imports
+from RosettaPy import Rosetta, RosettaScriptsVariableGroup, RosettaEnergyUnitAnalyser,
 
 # Create a Rosetta object with the desired parameters
 rosetta = Rosetta(
@@ -161,8 +163,8 @@ rosetta = Rosetta(
     job_id=...,
 )
 
-# Create tasks for each variant
-tasks = [
+# Run with the Rosetta tasks
+tasks = [ # Create tasks for each variant
     {
         "rsv": RosettaScriptsVariableGroup.from_dict(
             {
@@ -177,9 +179,13 @@ tasks = [
     for variant in variants
 ]
 
-# Run the Rosetta tasks
+# Run the tasks
 rosetta.run(inputs=tasks)
 
+# Or create a distributed runs with structure labels (-nstruct)
+options=[...] # Passing an optional list of options that will be used to all structure models
+rosetta.run(nstruct=nstruct, inputs=options)
+
 # Analyze the results
 analyser = RosettaEnergyUnitAnalyser(score_file=rosetta.output_scorefile_dir)
 best_hit = analyser.best_decoy
@@ -191,7 +197,7 @@ print(analyser.df.sort_values(by=analyser.score_term))
 
 print("-" * 79)
 
-print(f'Best Hit on this Rosetta run: {best_hit["decoy"]} - {best_hit["score"]}: {pdb_path}')
+print(f'Best Hit on this run: {best_hit["decoy"]} - {best_hit["score"]}: {pdb_path}')
 #
 ```
 

pyproject.toml

@@ -21,7 +21,6 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
-    "Programming Language :: Python :: 3.13"
 ]
 requires-python = ">=3.8"
 dynamic = ["version"]