add bump_version and bump version

conda.recipe/meta.yaml → .conda/meta.yaml

@@ -1,5 +1,4 @@
-{% set version = "1.2.10" %}
-
+{% set version = "1.2.11" %}
 package:
   name: "proteinflow"
   version: {{ version }}

.github/workflows/process-pull-request.yml

@@ -105,6 +105,7 @@ jobs:
         run: |
           git pull
           conda run -n proteinflow . make_docs.sh
+          echo ${{ needs.test.outputs.update }}
       - uses: stefanzweifel/git-auto-commit-action@v4
         if: ${{ needs.test.outputs.update }}
         with:

.github/workflows/python-publish.yml

@@ -16,6 +16,17 @@ permissions:
   contents: read
 
 jobs:
+  publish-to-conda:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: publish-to-conda
+      uses: MichaelsJP/[email protected]
+      with:
+        subDir: '.conda'
+        AnacondaToken: ${{ secrets.ANACONDA_TOKEN }}
+        override: true
+
   deploy:
 
     runs-on: ubuntu-latest

bump_version.py

@@ -0,0 +1,23 @@
+import click
+
+
+@click.option("--version", required=True)
+@click.command()
+def main(version):
+    with open("pyproject.toml", "r") as f:
+        lines = f.readlines()
+    with open("pyproject.toml", "w") as f:
+        for line in lines:
+            if line.startswith("version"):
+                line = f'version = "{version}"\n'
+            f.write(line)
+    with open(".conda/meta.yaml", "r") as f:
+        lines = list(f.readlines())
+    lines[0] = f'{{% set version = "{version}" %}}\n'
+    with open(".conda/meta.yaml", "w") as f:
+        for line in lines:
+            f.write(line)
+
+
+if __name__ == "__main__":
+    main()

docs/index.html

@@ -1225,6 +1225,8 @@ <h3 id="using-the-data">Using the data</h3>
     &#34;&#34;&#34;
 
     # download fasta files for excluded chains
+    if not os.path.exists(tmp_folder):
+        os.makedirs(tmp_folder)
     sequences = []
     for chain in exclude_chains:
         pdb_id, chain_id = chain.split(&#34;-&#34;)
@@ -1238,8 +1240,11 @@ <h3 id="using-the-data">Using the data</h3>
         os.remove(outfnm)
 
     # iterate over files in the dataset to check similarity
+    print(&#34;Checking excluded chains similarity...&#34;)
     exclude_biounits = []
-    for fn in os.listdir(os.path.join(local_datasets_folder, f&#34;proteinflow_{tag}&#34;)):
+    for fn in tqdm(
+        os.listdir(os.path.join(local_datasets_folder, f&#34;proteinflow_{tag}&#34;))
+    ):
         if not fn.endswith(&#34;.pickle&#34;):
             continue
         fp = os.path.join(local_datasets_folder, f&#34;proteinflow_{tag}&#34;, fn)

proteinflow/__init__.py

@@ -1095,6 +1095,8 @@ def _get_excluded_files(
     """
 
     # download fasta files for excluded chains
+    if not os.path.exists(tmp_folder):
+        os.makedirs(tmp_folder)
     sequences = []
     for chain in exclude_chains:
         pdb_id, chain_id = chain.split("-")
@@ -1108,8 +1110,11 @@ def _get_excluded_files(
         os.remove(outfnm)
 
     # iterate over files in the dataset to check similarity
+    print("Checking excluded chains similarity...")
     exclude_biounits = []
-    for fn in os.listdir(os.path.join(local_datasets_folder, f"proteinflow_{tag}")):
+    for fn in tqdm(
+        os.listdir(os.path.join(local_datasets_folder, f"proteinflow_{tag}"))
+    ):
         if not fn.endswith(".pickle"):
             continue
         fp = os.path.join(local_datasets_folder, f"proteinflow_{tag}", fn)

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "proteinflow"
-version = "1.2.10"
+version = "1.2.11"
 authors = [
     {name = "Liza Kozlova", email = "[email protected]"},
     {name = "Arthur Valentin", email = "[email protected]"}
@@ -36,4 +36,4 @@ keywords = ["bioinformatics", "dataset", "protein", "PDB", "deep learning"]
 proteinflow = "proteinflow.scripts.proteinflow_cli:cli"
 
 [tool.setuptools.packages]
-find = {}
+find = {}