Clean reqs

.github/workflows/_run_tests.yml

@@ -14,7 +14,7 @@ on:
         required: true
         type: string
 jobs:
-  pre-commit:
+  run-tests:
     runs-on: ${{ inputs.os }}
     steps:
     - uses: actions/checkout@v3

nbs_tests/model/model_interface.ipynb

@@ -485,7 +485,8 @@
    "outputs": [],
    "source": [
     "from peptdeep.model.ms2 import pDeepModel\n",
-    "from peptdeep.pretrained_models import MODEL_ZIP_FILE_PATH"
+    "from peptdeep.pretrained_models import MODEL_ZIP_FILE_PATH\n",
+    "from peptdeep.pretrained_models import download_models"
    ]
   },
   {
@@ -660,9 +661,11 @@
     }
    ],
    "source": [
+    "download_models()\n",
     "ms2_model = pDeepModel()\n",
     "ms2_model.build_from_py_codes(\n",
-    "    MODEL_ZIP_FILE_PATH, 'generic/ms2.pth.model.py', \n",
+    "    MODEL_ZIP_FILE_PATH,\n",
+    "    'generic/ms2.pth.model.py',\n",
     "    include_model_params_yaml=True\n",
     ")\n",
     "\n",

peptdeep/pretrained_models.py

@@ -64,7 +64,9 @@ def is_model_zip(downloaded_zip):
         return any(x == "generic/ms2.pth" for x in zip.namelist())
 
 
-def download_models(url: str = MODEL_URL, target_path: str = MODEL_ZIP_FILE_PATH):
+def download_models(
+    url: str = MODEL_URL, target_path: str = MODEL_ZIP_FILE_PATH, overwrite: bool = True
+):
     """
     Parameters
     ----------
@@ -77,30 +79,35 @@ def download_models(url: str = MODEL_URL, target_path: str = MODEL_ZIP_FILE_PATH
         Defaults to :data:`peptdeep.pretrained_models.MODEL_ZIP_FILE_PATH`
 
     overwrite : bool, optional
-        overwirte old model files.
+        overwrite old model files.
         Defaults to True.
 
     Raises
     ------
     FileNotFoundError
         If remote url is not accessible.
     """
+    if not overwrite and os.path.exists(target_path):
+        raise FileExistsError(f"Model file already exists: {target_path}")
+
     if not os.path.isfile(url):
         logging.info(f"Downloading {url} ...")
         try:
+            os.makedirs(os.path.dirname(target_path), exist_ok=True)
             context = ssl._create_unverified_context()
             requests = urllib.request.urlopen(url, context=context, timeout=10)
             with open(target_path, "wb") as f:
                 f.write(requests.read())
-        except (socket.timeout, urllib.error.URLError, urllib.error.HTTPError):
+        except Exception as e:
             raise FileNotFoundError(
                 "Downloading model failed! Please download the "
                 f'zip or tar file by yourself from "{url}",'
                 " and use \n"
                 f'"peptdeep --install-model /path/to/{LOCAL_MODAL_ZIP_NAME}.zip"\n'
                 " to install the models"
-            )
+            ) from e
     else:
+        os.makedirs(os.path.dirname(target_path), exist_ok=True)
         shutil.copy(url, target_path)
     logging.info(f"The pretrained models had been downloaded in {target_path}")
 

requirements/requirements.txt

@@ -8,7 +8,6 @@ torch==2.5.1
 tqdm==4.67.1
 numba==0.60.0
 psutil==6.1.0
-biopython==1.84
 transformers==4.47.0
 scikit-learn==1.6.0
 lxml==5.3.0

requirements/requirements_gui.txt

@@ -1,3 +1,2 @@
-
 streamlit==1.40.2
 streamlit-aggrid==1.0.5

requirements/requirements_gui_loose.txt

@@ -1,3 +1,2 @@
-
 streamlit>=1.23.0 # test: tolerate_version
 streamlit-aggrid

requirements/requirements_loose.txt

@@ -8,7 +8,6 @@ torch
 tqdm
 numba
 psutil
-biopython
 transformers
 scikit-learn
 lxml