Finalized docs

pachterlab · May 15, 2023 · a254c9a · a254c9a
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diff --git a/docs/src/setup.md b/docs/src/setup.md
@@ -5,7 +5,7 @@ Function to install/download third-party dependencies for a specified gget modul
 
 **Positional argument**  
 `module`  
-gget module for which dependencies should be installed (currently only "alphafold").  
+gget module for which dependencies should be installed ("alphafold", "gpt" or "cellxgene").  
 
 ### Example
 ```bash

diff --git a/docs/src/updates.md b/docs/src/updates.md
@@ -1,5 +1,8 @@
 ## ✨ What's new  
-**Version ≥ 0.27.6** (May 1, 2023):  
+**Version ≥ 0.27.7** (May 15, 2023):  
+- Moved dependencies for modules [`gget gpt`](./gpt.md) and [`gget cellxgene`](./cellxgene.md) from automatically installed requirements to [`gget setup`](./setup.md).  
+
+**Version ≥ 0.27.6** (May 1, 2023) (YANKED):  
 - Thanks to PR by [Tomás Di Domenico](https://github.com/tdido): [`gget search`](./search.md) can now also query plant 🌱 Ensembl IDs.  
 - New module: [`gget cellxgene`](./cellxgene.md)  
 

diff --git a/gget/gget_setup.py b/gget/gget_setup.py
@@ -34,13 +34,14 @@
 PARAMS_PATH = os.path.join(PARAMS_DIR, "params_temp.tar")
 
 
-def setup(module):
+def setup(module, verbose=True):
     """
     Function to install third-party dependencies for a specified gget module.
     Requires pip to be installed (https://pip.pypa.io/en/stable/installation).
 
     Args:
     - module    (str) gget module for which dependencies should be installed, e.g. "alphafold", "cellxgene" or "gpt".
+    - verbose   True/False whether to print progress information. Default True.
     """
     supported_modules = ["alphafold", "cellxgene", "gpt"]
     if module not in supported_modules:
@@ -49,7 +50,8 @@ def setup(module):
         )
 
     if module == "gpt":
-        logging.info("Installing openai package (requires pip).")
+        if verbose:
+            logging.info("Installing openai package (requires pip).")
         command = "pip install -q -U openai"
         with subprocess.Popen(command, shell=True, stderr=subprocess.PIPE) as process:
             stderr = process.stderr.read().decode("utf-8")
@@ -67,15 +69,17 @@ def setup(module):
         try:
             import openai
 
-            logging.info(f"openai installed succesfully.")
+            if verbose:
+                logging.info(f"openai installed succesfully.")
         except ImportError as e:
             logging.error(
                 f"openai installation with pip (https://pypi.org/project/openai) failed. Import error:\n{e}"
             )
             return
 
     if module == "cellxgene":
-        logging.info("Installing cellxgene-census package (requires pip).")
+        if verbose:
+            logging.info("Installing cellxgene-census package (requires pip).")
         command = "pip install -q -U cellxgene-census"
         with subprocess.Popen(command, shell=True, stderr=subprocess.PIPE) as process:
             stderr = process.stderr.read().decode("utf-8")
@@ -93,7 +97,8 @@ def setup(module):
         try:
             import cellxgene_census
 
-            logging.info(f"cellxgene_census installed succesfully.")
+            if verbose:
+                logging.info(f"cellxgene_census installed succesfully.")
         except ImportError as e:
             logging.error(
                 f"cellxgene-census installation with pip (https://pypi.org/project/cellxgene-census) failed. Import error:\n{e}"
@@ -102,7 +107,7 @@ def setup(module):
 
     if module == "alphafold":
         if platform.system() == "Windows":
-            logging.warning(
+            logging.error(
                 "gget setup alphafold and gget alphafold are not supported on Windows OS."
             )
 
@@ -118,7 +123,8 @@ def setup(module):
             # if openmm.__version__ != "7.5.1":
             #     raise ImportError()
 
-            # logging.info(f"openmm v{openmm.__version__} already installed.")
+            # if verbose:
+            #   logging.info(f"openmm v{openmm.__version__} already installed.")
 
         except ImportError as e:
             raise ImportError(
@@ -133,7 +139,8 @@ def setup(module):
             )
 
         ## Install py3Dmol
-        logging.info("Installing py3Dmol (requires pip).")
+        if verbose:
+            logging.info("Installing py3Dmol (requires pip).")
         command = "pip install -q py3Dmol"
         with subprocess.Popen(command, shell=True, stderr=subprocess.PIPE) as process:
             stderr = process.stderr.read().decode("utf-8")
@@ -151,15 +158,17 @@ def setup(module):
         try:
             import py3Dmol
 
-            logging.info(f"py3Dmol installed succesfully.")
+            if verbose:
+                logging.info(f"py3Dmol installed succesfully.")
         except ImportError as e:
             logging.error(
                 f"py3Dmol installation with pip (https://pypi.org/project/py3Dmol/) failed. Import error:\n{e}"
             )
             return
 
         ## Install Alphafold if not already installed
-        logging.info("Installing AlphaFold from source (requires pip and git).")
+        if verbose:
+            logging.info("Installing AlphaFold from source (requires pip and git).")
 
         ## Install AlphaFold and change jackhmmer directory where database chunks are saved in
         # Define AlphaFold folder name and location
@@ -226,7 +235,8 @@ def setup(module):
         try:
             import alphafold as AlphaFold
 
-            logging.info(f"AlphaFold installed succesfully.")
+            if verbose:
+                logging.info(f"AlphaFold installed succesfully.")
         except ImportError as e:
             logging.error(f"AlphaFold installation failed. Import error:\n{e}")
             return
@@ -237,7 +247,8 @@ def setup(module):
             sys.path.append(alphafold_path)
 
         ## Install pdbfixer
-        logging.info("Installing pdbfixer from source (requires pip and git).")
+        if verbose:
+            logging.info("Installing pdbfixer from source (requires pip and git).")
 
         pdbfixer_folder = os.path.join(
             PACKAGE_PATH, "tmp_pdbfixer_" + str(uuid.uuid4())
@@ -288,9 +299,10 @@ def setup(module):
             os.makedirs(os.path.join(PARAMS_DIR, "params/"), exist_ok=True)
 
         if len(os.listdir(os.path.join(PARAMS_DIR, "params/"))) < 12:
-            logging.info(
-                "Downloading AlphaFold model parameters (requires 4.1 GB of storage). This might take a few minutes."
-            )
+            if verbose:
+                logging.info(
+                    "Downloading AlphaFold model parameters (requires 4.1 GB of storage). This might take a few minutes."
+                )
             if platform.system() == "Windows":
                 # The double-quotation marks allow white spaces in the path, but this does not work for Windows
                 command = f"""
@@ -317,6 +329,8 @@ def setup(module):
                 logging.error("Model parameter download failed.")
                 return
             else:
-                logging.info("Model parameter download complete.")
+                if verbose:
+                    logging.info("Model parameter download complete.")
         else:
-            logging.info("AlphaFold model parameters already downloaded.")
+            if verbose:
+                logging.info("AlphaFold model parameters already downloaded.")
diff --git a/gget/main.py b/gget/main.py
@@ -906,6 +906,15 @@ def main():
         help="gget module for which dependencies should be installed, e.g. 'alphafold'",
     )
 
+    parser_setup.add_argument(
+        "-q",
+        "--quiet",
+        default=True,
+        action="store_false",
+        required=False,
+        help="Does not print progress information.",
+    )
+
     ## gget alphafold subparser
     alphafold_desc = "Predicts the structure of a protein using a simplified version of AlphaFold v2.3.0 (https://doi.org/10.1038/s41586-021-03819-2)."
     parser_alphafold = parent_subparsers.add_parser(
@@ -1148,6 +1157,14 @@ def main():
         required=False,
         help="The file name to save the generated text to (defaults to printing the output to the console)",
     )
+    parser_gpt.add_argument(
+        "-q",
+        "--quiet",
+        default=True,
+        action="store_false",
+        required=False,
+        help="Do not print progress information.",
+    )
 
     # cellxgene parser arguments
     cellxgene_desc = (
@@ -1501,6 +1518,7 @@ def main():
             frequency_penalty=args.frequency_penalty,
             logit_bias=args.logit_bias,
             out=args.out,
+            verbose=args.quiet,
         )
 
         if args.out is None:
@@ -1677,7 +1695,7 @@ def main():
         if not args.fasta_deprecated and not args.fasta:
             parser_muscle.error("the following arguments are required: fasta")
 
-        muscle(fasta=args.fasta, super5=args.super5, out=args.out)
+        muscle(fasta=args.fasta, super5=args.super5, out=args.out, verbose=args.quiet)
 
     ## ref return
     if args.command == "ref":
@@ -2047,7 +2065,7 @@ def main():
 
     ## setup return
     if args.command == "setup":
-        setup(args.module)
+        setup(args.module, verbose=args.quiet)
 
     ## alphafold return
     if args.command == "alphafold":
@@ -2067,6 +2085,7 @@ def main():
             relax=args.relax,
             plot=False,
             show_sidechains=False,
+            verbose=args.quiet,
         )
 
     ## pdb return