Fix FTP URLs for PRIDE and MassIVE (#31)

* Fixed links for all the things

* Fix most linting errors

* Migrate to Ruff

* Used Ruff to reformat

* Change branch target

* Update test action

* Migrate to pyproject.toml

* Bump changelog

* Add codecov token

.github/workflows/lint.yml

@@ -0,0 +1,30 @@
+name: Lint
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install Ruff
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+
+      - name: Lint with Ruff
+        run: |
+          ruff check . --output-format=github
+
+      - name: Check formatting with Ruff
+        run: |
+          ruff format --check .

.github/workflows/tests.yml

@@ -20,26 +20,21 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.8
+    - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: "3.8"
+        python-version: "3.10"
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install flake8 pytest pytest-cov wheel
         pip install -e .
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Run unit and system tests
       run: |
         pytest --cov=ppx tests/
     - name: Upload coverage to codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v4
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: true

.pre-commit-config.yaml

@@ -1,6 +1,19 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 22.3.0 # Replace by any tag/version: https://github.com/psf/black/tags
-    hooks:
-      - id: black
-        language_version: python3 # Should be a command that runs python3.6+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+  - id: check-toml
+  - id: check-yaml
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+  - id: detect-private-key
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.3.7
+  hooks:
+    # Run the linter.
+    - id: ruff
+      types_or: [ python, pyi, jupyter ]
+      args: [ --fix, --show-fixes ]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [ python, pyi, jupyter ]

CHANGELOG.md

@@ -1,12 +1,18 @@
 # Changelog for ppx
 
-## [Unreleased]
+## [1.4.0]
+### Changed
+- Linting and formatting is now performed with Ruff.
+- Migrated to pyproject.toml based build.
+
 ### Fixed
+- Fixed MassIVE FTP URLs using the MassIVE PROXI API.
+- Fixed PRIDE FTP URLs... again.
 - Updated unit tests with new PRIDE FTP URLs.
 
 ## [1.3.0] - 2022-04-39
 ### Added
-- Support for cloud provider destinations. Thanks @sooheon! 
+- Support for cloud provider destinations. Thanks @sooheon!
 
 ## [1.2.6] - 2022-03-16
 ### Fixed
@@ -45,25 +51,25 @@
 
 ## [1.2.0] - 2021-09-14
 ### Added
-- New `timeout` parameter for most functions and classes. This specifies the 
+- New `timeout` parameter for most functions and classes. This specifies the
   maximum amount of time to wait for a response from the server.
 
 ### Changed
 - The backend for MassIVE now uses the GNPS API to list files and projects,
-  only falling back to scraping the FTP server on failure. This should make 
+  only falling back to scraping the FTP server on failure. This should make
   it much faster. Thanks @mwang87!
 - Files and projects are now returned in sorted order.
 
 ### Fixed
-- Poor connections with PRIDE were leading to a number of occasional errors. 
-  Multiple reconnect attempts are now tried for a wider variety of FTP 
+- Poor connections with PRIDE were leading to a number of occasional errors.
+  Multiple reconnect attempts are now tried for a wider variety of FTP
   operations.
 
 ## [1.1.1] - 2021-07-02
 ### Fixed
 - Downloading files is now more robust. ppx will now retry FTP connections up
   to 10 times if the connection was dropped or refused.
-- Partial downloads are now continued automatically by comparing the local 
+- Partial downloads are now continued automatically by comparing the local
   file size to the remote file size.
 
 ## [1.1.0] - 2021-05-18
@@ -73,26 +79,25 @@
   instead. **Note that this may change the number, identity, and order of the
   file that were previously returned for PRIDE projects!**
 - Small documentation updates.
-  
+
 ### Added
-- Caching of the remote files and directories found for a project. If a 
+- Caching of the remote files and directories found for a project. If a
   project's `fetch` attribute is `False`, then we'll rely on this cached
   data, so long as it is available. Setting `fetch=True` will always refresh
   the data from the repository.
 
-## [1.0.0] - 2021-05-14  
-### Changed  
+## [1.0.0] - 2021-05-14
+### Changed
 - **We did a complete rework of the API!** This will break nearly all previous
   code using ppx, but greatly improves its versatility.
   See the [docs](https://ppx.readthedocs.io) for more details
 - Updated the build to align with
   [PEP517](https://www.python.org/dev/peps/pep-0517/)
-  
+
 ### Added
-- A command line interface for downloading files from PRIDE and MassIVE 
+- A command line interface for downloading files from PRIDE and MassIVE
   projects.
 - Additional unit tests.
 - A ppx logo
 - This changelog.
 - ppx is now available on bioconda!
-

docs/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #
@@ -13,8 +12,8 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
-import sys
 import subprocess
+import sys
 
 sys.path.insert(0, os.path.abspath(".."))
 

ppx/__init__.py

@@ -1,23 +1,23 @@
 """See the README for detailed documentation and examples."""
+
 try:
-    from importlib.metadata import version, PackageNotFoundError
+    from importlib.metadata import PackageNotFoundError, version
 
     try:
         __version__ = version(__name__)
     except PackageNotFoundError:
         pass
 
 except ImportError:
-    from pkg_resources import get_distribution, DistributionNotFound
+    from pkg_resources import DistributionNotFound, get_distribution
 
     try:
         __version__ = get_distribution(__name__).version
     except DistributionNotFound:
         pass
 
-from . import pride
-from . import massive
+from . import massive, pride
+from .config import get_data_dir, set_data_dir
 from .factory import find_project
-from .pride import PrideProject
 from .massive import MassiveProject
-from .config import get_data_dir, set_data_dir
+from .pride import PrideProject

ppx/config.py

@@ -1,6 +1,7 @@
 """This module contains the configuration details for ppx"""
-import os
+
 import logging
+import os
 from pathlib import Path
 
 from cloudpathlib import AnyPath
@@ -14,6 +15,7 @@ class PPXConfig:
     Attributes
     ----------
     path : pathlib.Path object
+
     """
 
     def __init__(self):
@@ -61,6 +63,7 @@ def _resolve_path(path):
         -------
         Path or CloudPath
             The resolved path.
+
         """
         path = AnyPath(path)
         try:
@@ -83,6 +86,7 @@ def set_data_dir(path=None):
     ----------
     path : str or pathlib.Path object, optional
         The path for ppx to use as its data directory.
+
     """
     config.path = path
 

ppx/factory.py

@@ -1,15 +1,16 @@
+"""The PXDataset class and its associated methods.
+
+This is the foundation of the ppx package.
 """
-This module contains the PXDataset class and its associated methods,
-which are the foundation of the ppx package.
-"""
-import re
+
 import logging
+import re
 from urllib.parse import urlparse
 
 import requests
 
-from .pride import PrideProject
 from .massive import MassiveProject
+from .pride import PrideProject
 
 LOGGER = logging.getLogger(__name__)
 
@@ -29,6 +30,7 @@ class PXDFactory:
         Should ppx check the remote repository for updated metadata?
     timeout : float, optional
         The maximum amount of time to wait for a server response.
+
     """
 
     rest = "http://proteomecentral.proteomexchange.org/cgi/GetDataset"
@@ -77,11 +79,11 @@ def id(self):
 
     def find(self):
         """Find the dataset at the partner repository"""
-        kwargs = dict(
-            local=self._local,
-            fetch=self._fetch,
-            timeout=self._timeout,
-        )
+        kwargs = {
+            "local": self._local,
+            "fetch": self._fetch,
+            "timeout": self._timeout,
+        }
 
         if self._repo == "PRIDE":
             return PrideProject(self._repo_id, **kwargs)
@@ -156,13 +158,14 @@ def find_project(identifier, local=None, repo=None, fetch=False, timeout=10.0):
     -------
     :py:class:`~ppx.PrideProject` or :py:class:`~ppx.MassiveProject`
         An object to interact with the project data in the repository.
+
     """
     identifier = str(identifier).upper()
     if repo is not None:
         repo = str(repo).lower()
 
     # User-specified:
-    kwargs = dict(local=local, fetch=fetch, timeout=timeout)
+    kwargs = {"local": local, "fetch": fetch, "timeout": timeout}
     if repo == "pride":
         return PrideProject(identifier, **kwargs)