dayhoff-tools 1.14.15__py3-none-any.whl → 1.15.1__py3-none-any.whl

dayhoff_tools/embedders.py

@@ -179,8 +179,8 @@ class H5Reformatter(Processor):
     def embedding_file_to_df(self, file_name: str) -> pd.DataFrame:
         with h5py.File(file_name, "r") as f:
             gene_names = list(f.keys())
-            Xg = [f[key][()] for key in gene_names]  # type:ignore
-        return pd.DataFrame(np.asmatrix(Xg), index=gene_names)  # type:ignore
+            Xg = [f[key][()] for key in gene_names]  # type: ignore
+        return pd.DataFrame(np.asmatrix(Xg), index=gene_names)  # type: ignore
 
     def write_df_to_h5(self, df: pd.DataFrame, filename: str, description: str) -> None:
         """

dayhoff_tools/fasta.py

@@ -857,14 +857,12 @@ def fasta_to_sqlite(fasta_file: str, db_file: str, batch_size: int = 1000) -> No
     # Create the SQLite database and table
     print("Creating SQLite database...")
     with sqlite3.connect(db_file) as conn:
-        conn.execute(
-            """
+        conn.execute("""
             CREATE TABLE IF NOT EXISTS proteins (
                 protein_id TEXT PRIMARY KEY,
                 sequence TEXT NOT NULL
             )
-        """
-        )
+        """)
     print("Database created successfully.")
 
     # Estimate number of records for progress bar

dayhoff_tools/intake/kegg.py

@@ -25,9 +25,7 @@ def get_ko2gene_df(db: str, ko: str | list[str] | None = None) -> pd.DataFrame:
         query = (
             f"SELECT gene,ko FROM gene_to_ko WHERE ko IN ({','.join('?' * len(ko))})"
         )
-        result_df = pd.read_sql_query(
-            query, conn, params=ko  # type:ignore
-        )
+        result_df = pd.read_sql_query(query, conn, params=ko)  # type: ignore
     else:
         query = f"SELECT gene,ko FROM gene_to_ko"
         result_df = pd.read_sql_query(query, conn)

dayhoff_tools/intake/structure.py

@@ -409,10 +409,10 @@ class PDBFolderProcessor:
     def _get_pdb_files(self) -> list[str]:
         """
         Get a list of PDB files in the specified directory, optionally filtered by ID set.
-        Files are sorted by creation time to ensure consistent processing order.
+        Files are sorted alphabetically to ensure consistent, reproducible processing order.
 
         Returns:
-            List of PDB file names sorted by creation time.
+            List of PDB file names sorted alphabetically.
         """
         print("Scanning directory for PDB files...")
         pdb_files = [
@@ -424,8 +424,8 @@ class PDBFolderProcessor:
                 f for f in pdb_files if self._extract_id_from_filename(f) in self.id_set
             ]
 
-        # Sort files by creation time
-        pdb_files.sort(key=lambda f: os.path.getctime(os.path.join(self.pdb_dir, f)))
+        # Sort files alphabetically for deterministic, reproducible order
+        pdb_files.sort()
 
         print(f"Found {len(pdb_files)} PDB files")
         return pdb_files

{dayhoff_tools-1.14.15.dist-info → dayhoff_tools-1.15.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dayhoff-tools
-Version: 1.14.15
+Version: 1.15.1
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com
@@ -40,8 +40,8 @@ Requires-Dist: sqlalchemy (>=2.0.40,<3.0.0) ; extra == "full"
 Requires-Dist: toml (>=0.10)
 Requires-Dist: tqdm (>=4.67.1) ; extra == "embedders"
 Requires-Dist: tqdm (>=4.67.1) ; extra == "full"
-Requires-Dist: transformers (==4.36.2) ; extra == "full"
 Requires-Dist: transformers (>=4.36.2) ; extra == "embedders"
+Requires-Dist: transformers (>=4.36.2) ; extra == "full"
 Requires-Dist: typer (>=0.9.0)
 Requires-Dist: tzdata (>=2025.2)
 Description-Content-Type: text/markdown

{dayhoff_tools-1.14.15.dist-info → dayhoff_tools-1.15.1.dist-info}/RECORD

@@ -2,7 +2,7 @@ dayhoff_tools/__init__.py,sha256=M5zThPyEBRYa5CfwlzKhcqTevWn3OKu62cjV6Zqie2A,469
 dayhoff_tools/batch/__init__.py,sha256=N7v1pUg3rp68W6J7cX2Gssxdfp57Z7G0WeFJh7gKeiM,163
 dayhoff_tools/batch/workers/__init__.py,sha256=DJTtiBSE5k9J6qwG_MsXDn8hgz_lvEdaMwqKa6YyqXo,369
 dayhoff_tools/batch/workers/base.py,sha256=ZveUds6GW-aInj9LL0_VEYkXxOyZWRcOeJdacnEb8xo,5346
-dayhoff_tools/batch/workers/boltz.py,sha256=breCGITkX-_Xj9I_C1R-mKkG9RUCzSw3Kcdbbx_S5LA,18405
+dayhoff_tools/batch/workers/boltz.py,sha256=-_rgUvKcYfrCgBLpM-eIgWXvne6UJa2MqUFyllNRLUc,18397
 dayhoff_tools/batch/workers/embed_t5.py,sha256=A5WqsQa1WZ7_la5X5wt0XUP-VwOglH04WyEINhwipeY,2750
 dayhoff_tools/chemistry/standardizer.py,sha256=uMn7VwHnx02nc404eO6fRuS4rsl4dvSPf2ElfZDXEpY,11188
 dayhoff_tools/chemistry/utils.py,sha256=jt-7JgF-GeeVC421acX-bobKbLU_X94KNOW24p_P-_M,2257
@@ -11,16 +11,16 @@ dayhoff_tools/cli/batch/__init__.py,sha256=0QMxkelGUdvdd7-P-WG8YX2h0qjkKKb-0JbEH
 dayhoff_tools/cli/batch/aws_batch.py,sha256=DOp8KvmTrie15O61DP1HT13PSr3s5imxM-VZHvaLO7Q,15174
 dayhoff_tools/cli/batch/commands/__init__.py,sha256=1xRzzL_mc1hz1Pv0OWNr-g6fkL5XbEsOTGHzrqddLCA,458
 dayhoff_tools/cli/batch/commands/boltz.py,sha256=N0LksmtOpkvnEsR0SAUHxtksKPAsQjR83h3Cis14nz4,12085
-dayhoff_tools/cli/batch/commands/cancel.py,sha256=kjvmCcFaMShyHfQjvR4WlII4njg4Fm4uffpWcY1qRWg,5299
-dayhoff_tools/cli/batch/commands/clean.py,sha256=nWOKbVM2nDuLMpyC038Q9aylOQxk2bq4N0JF65qJg-s,4570
-dayhoff_tools/cli/batch/commands/embed_t5.py,sha256=QXFydAw0wndevdzXF1cxikxMmvn1BuQ5p9lwutQFajU,11453
-dayhoff_tools/cli/batch/commands/finalize.py,sha256=OQUF9RiO8S55SCeQcFqExLKjYd-leL0Z_FOV0xMg7Dw,13497
+dayhoff_tools/cli/batch/commands/cancel.py,sha256=GDrfidzmIB9FFTpi3Jjzgp3NCbVvbIhamo3lCfjQemI,5343
+dayhoff_tools/cli/batch/commands/clean.py,sha256=0EhpgG9ohsegDumUYhgKlWdIcPfKnEJfK2CnfT9azjk,4606
+dayhoff_tools/cli/batch/commands/embed_t5.py,sha256=FfuiMgkw0BMmxD5rw78G-U0Sn_goK4F6E_ItSYp9pr8,11452
+dayhoff_tools/cli/batch/commands/finalize.py,sha256=vSruaD8rMZFd7VRvtNjJ0gXR0239jxZfmwrgC3WglCU,13666
 dayhoff_tools/cli/batch/commands/list_jobs.py,sha256=COfxZddDVUAHeTayNAB3ruYNhgrE3osgFxY2qzf33cg,4284
 dayhoff_tools/cli/batch/commands/local.py,sha256=dZeKhNakaM1jS-EoByAwg1nWspRRoOmYzcwzjEKBaIA,3226
 dayhoff_tools/cli/batch/commands/logs.py,sha256=ctgJksdzFmqBdD18ePPsZe2BpuJYtHz2xAaMPnUplmQ,5293
 dayhoff_tools/cli/batch/commands/retry.py,sha256=JgOMiwuESNG4Wp_fQ_vxy1RwyOZPt_kmVbLYdxYTVBY,9897
-dayhoff_tools/cli/batch/commands/status.py,sha256=4kfii7mgtJKXWwZDsR4mtb_dQgCdryGkGEjNOpDxTT0,13404
-dayhoff_tools/cli/batch/commands/submit.py,sha256=AXbvSReN8fLlzR5swE81pH7yvbCC1GUMCbsDrfoHAws,6786
+dayhoff_tools/cli/batch/commands/status.py,sha256=Oneci0Wv4dfF5SoThSFyE9BTqaN_u9yhGSecC7x0rd8,13512
+dayhoff_tools/cli/batch/commands/submit.py,sha256=ykbbXniMzgKpY0iRmrGxwOU6e4-lPXkfyJ_HQ7AyTik,6785
 dayhoff_tools/cli/batch/job_id.py,sha256=mqr8SwcPlUWIYLaR_C4kACmL2ZFK8jaddd7B-45-XaQ,4246
 dayhoff_tools/cli/batch/manifest.py,sha256=eLyiOFXonAUh5rfHcXyR2CzmRKXQz9-tTbJcWnVbbmE,8857
 dayhoff_tools/cli/cloud_commands.py,sha256=xrWQZm48e09GTh8RmYh3JqXUzW8mMy07dHk_77LqZx8,41199
@@ -48,9 +48,9 @@ dayhoff_tools/cli/engines_studios/simulators/studio_status_simulator.py,sha256=6
 dayhoff_tools/cli/engines_studios/ssh_config.py,sha256=UCv-jf_zSuk7FUStkCQBAJz1QkxiSEwZbdSrwt_9SMU,2932
 dayhoff_tools/cli/engines_studios/studio_commands.py,sha256=KGSNZQS8MmM_DfQzT9SRZvuR3OK6NdIdOrqI2wJFyes,25984
 dayhoff_tools/cli/github_commands.py,sha256=pfrxI68LObGm_gtPlQN-gHPahHV4l9k9T4GqO99NNL0,8948
-dayhoff_tools/cli/main.py,sha256=6ffnaFzui-bVd1ME7yThk_ZrMOofwStamEUkkYlminY,8503
+dayhoff_tools/cli/main.py,sha256=E4UXtOBRRAhcrJ3RgLCQFpJdamFN-p9xViMkX45kNgw,6456
 dayhoff_tools/cli/swarm_commands.py,sha256=5EyKj8yietvT5lfoz8Zx0iQvVaNgc3SJX1z2zQR6o6M,5614
-dayhoff_tools/cli/utility_commands.py,sha256=O6vy3rONTeuPYZyhjnFeqf8GxUlyc7i2O11d1s3shH4,45513
+dayhoff_tools/cli/utility_commands.py,sha256=Zaib879sJ8xD-RV42dSaaxdVC_lP6mLSJ-yTF5eU-pQ,9832
 dayhoff_tools/deployment/base.py,sha256=uZnFvnPQx6pH_HmJbdThweAs3BrxMaDohpE3iX_-yk4,18377
 dayhoff_tools/deployment/deploy_aws.py,sha256=1j16aE4hmln4pQVtcSGuIGVWbOBfWwveytvihjofADo,21519
 dayhoff_tools/deployment/deploy_gcp.py,sha256=xgaOVsUDmP6wSEMYNkm1yRNcVskfdz80qJtCulkBIAM,8860
@@ -58,20 +58,20 @@ dayhoff_tools/deployment/deploy_utils.py,sha256=KyUFZZWn8NGT9QpR0HGqkX-huOFubvYC
 dayhoff_tools/deployment/job_runner.py,sha256=hljvFpH2Bw96uYyUup5Ths72PZRL_X27KxlYzBMgguo,5086
 dayhoff_tools/deployment/processors.py,sha256=LM0CQbr4XCb3AtLbrcuDQm4tYPXsoNqgVJ4WQYDjzJc,12406
 dayhoff_tools/deployment/swarm.py,sha256=YJfvVOcAS8cYcIj2fiN4qwC2leh0I9w5A4px8ZWSF6g,22833
-dayhoff_tools/embedders.py,sha256=1THnmio4FYkBswy_xkIiwT-ZOEMn6ZLbTAa-Uz0-kyE,36615
-dayhoff_tools/fasta.py,sha256=USdemH4c_dNhWXOTAhldvlDi8eLHogsy0YSrOnODB5I,50773
+dayhoff_tools/embedders.py,sha256=4o49Zm0gPxGcBcofTCZMC_6IUaOOTbTY2xmVadrX_ss,36617
+dayhoff_tools/fasta.py,sha256=tmuQ8BGpMqaDF9pJCro8roqpQsD9qeTnodNvXJmgH9w,50751
 dayhoff_tools/file_ops.py,sha256=JlGowvr-CUJFidV-4g_JmhUTN9bsYuaxtqKmnKomm-Q,8506
 dayhoff_tools/h5.py,sha256=j1nxxaiHsMidVX_XwB33P1Pz9d7K8ZKiDZwJWQUUQSY,21158
 dayhoff_tools/intake/gcp.py,sha256=uCeEskhbEwJIYpN6ne6siT1dbpTizCjjel-hRe0kReE,3030
 dayhoff_tools/intake/gtdb.py,sha256=58JNLWpr3LkXiIq-ubAcEFeR5DyN9YrA-YEoQI_FzlA,10608
-dayhoff_tools/intake/kegg.py,sha256=SaVbumB4leNTSevamT29yIqHurejw1wmcCC32D5Qyco,965
+dayhoff_tools/intake/kegg.py,sha256=Cv1ar9X2aFd25VDqn-3zMZ0epgtMc-uFKUIYgvwxC6U,944
 dayhoff_tools/intake/mmseqs.py,sha256=uEYzRsthJAlUeRYNCfFtJFE73SbuhfUIS1ygYFkhmtw,6435
-dayhoff_tools/intake/structure.py,sha256=ufN3gAodQxhnt7psK1VTQeu9rKERmo_PhoxIbB4QKMw,27660
+dayhoff_tools/intake/structure.py,sha256=d-H9UFSJSfdp1zzp_F0lDBrMdCv3yQXl6HOVCE16u3E,27645
 dayhoff_tools/intake/uniprot.py,sha256=BZYJQF63OtPcBBnQ7_P9gulxzJtqyorgyuDiPeOJqE4,16456
 dayhoff_tools/logs.py,sha256=DKdeP0k0kliRcilwvX0mUB2eipO5BdWUeHwh-VnsICs,838
 dayhoff_tools/sqlite.py,sha256=jV55ikF8VpTfeQqqlHSbY8OgfyfHj8zgHNpZjBLos_E,18672
 dayhoff_tools/warehouse.py,sha256=UETBtZD3r7WgvURqfGbyHlT7cxoiVq8isjzMuerKw8I,24475
-dayhoff_tools-1.14.15.dist-info/METADATA,sha256=YBP4lpBDAIhxYuJ65DR_ADrajk6hyLC1e_UCVc_bwx8,3136
-dayhoff_tools-1.14.15.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
-dayhoff_tools-1.14.15.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.14.15.dist-info/RECORD,,
+dayhoff_tools-1.15.1.dist-info/METADATA,sha256=QSQwSam7GhLoduhoXHgrPYJnECe74Jym7LntG3tQou4,3135
+dayhoff_tools-1.15.1.dist-info/WHEEL,sha256=kJCRJT_g0adfAJzTx2GUMmS80rTJIVHRCfG0DQgLq3o,88
+dayhoff_tools-1.15.1.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.15.1.dist-info/RECORD,,

{dayhoff_tools-1.14.15.dist-info → dayhoff_tools-1.15.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.3.0
+Generator: poetry-core 2.3.1
 Root-Is-Purelib: true
 Tag: py3-none-any