Merge pull request #79 from Noble-Lab/pypi-release

Update for PyPI release

Author: bittremieux

.github/workflows/black.yml

@@ -7,10 +7,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Setup Python 3.8
+      - name: Setup Python 3.10
         uses: actions/setup-python@v2
         with:
-          python-version: "3.8"
+          python-version: "3.10"
 
       - name: Run black
         uses: psf/black@stable

.github/workflows/tests.yml

@@ -5,11 +5,9 @@ name: tests
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
-    branches: [ master ]
-  schedule:
-  - cron: "0 0 1 1/1 *" # Run monthly
+    branches: [ main ]
 
 jobs:
   build:
@@ -20,16 +18,16 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       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 .
+        pip install -e .[dev]
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -38,8 +36,8 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Run unit and system tests
       run: |
-        pytest --cov=ppx tests/
+        pytest --cov=casanovo tests/
     - name: Upload coverage to codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         fail_ci_if_error: true

CHANGELOG.md

@@ -5,9 +5,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
-
 ### Added
-
+- The first PyPI release! :tada:
+- Tests are run on every PR automatically.
+- Test code coverage must be maintained or improved with each change.
 - Log the active Casanovo configuration.
 - Log to both the console and a log file.
 - Use all available hardware resources (GPU and CPU).

CONTRIBUTING.md

@@ -1,9 +1,9 @@
-# Contributing to casanovo
+# Contributing to Casanovo
 
 First off, thank you for taking the time to contribute.
 
 The following document provides guidelines for contributing to the
-documentation and the code of casanovo. **No contribution is too small!** Even
+documentation and the code of Casanovo. **No contribution is too small!** Even
 fixing a simple typo in the documentation is immensely helpful.
 
 
@@ -20,7 +20,7 @@ There are three exceptions to this:
 2. The Vignettes are created from Jupyter notebooks.
 
 3. The Code of Conduct, Release Notes, and this Contributing document are 
-   markdown files that live in the root of the casanovo repository.
+   markdown files that live in the root of the Casanovo repository.
 
 ### Editing most documents
 
@@ -39,14 +39,14 @@ way.
 
 ## Contributing to the code
 
-We welcome contributions to the source code of casanovo---particularly 
-ones that address discussed [issues](https://github.com/Noble-Lab/casanovo/issues).
+We welcome contributions to the source code of Casanovo---particularly 
+ones that address discussed [issues](https://github.com/Noble-Lab/Casanovo/issues).
 
-Contributions to casanovo follow a standard GitHub contribution workflow:
+Contributions to Casanovo follow a standard GitHub contribution workflow:
 
-1. Create your own fork of the casanovo repository on GitHub.
+1. Create your own fork of the Casanovo repository on GitHub.
 
-2. Clone your forked casanovo repository to work on locally.
+2. Clone your forked Casanovo repository to work on locally.
 
 3. Create a new branch with a descriptive name for your changes:
 
@@ -59,19 +59,19 @@ git checkout -b fix_x
 5. Add, commit, and push your changes to your forked repository.
 
 6. On the GitHub page for you forked repository, click "Pull request" to propose
-   adding your changes to casanovo.
+   adding your changes to Casanovo.
 
 7. We'll review, discuss, and help you make any revisions that are required. If
-   all goes well, your changes will be added to casanovo
+   all goes well, your changes will be added to Casanovo
    in the next release!
 
 
 ### Python code style
 
-The casanovo project follows the [PEP 8
+The Casanovo project follows the [PEP 8
 guidelines](https://www.python.org/dev/peps/pep-0008/) for Python code style.
 More specifically, we use [black](https://black.readthedocs.io/en/stable/) to
-format code and lint Python code in casanovo.
+format code and lint Python code in Casanovo.
 
 We highly recommend setting up a pre-commit hook for black. This will run black
 on all of the Python source files before the changes can be committed. Because
@@ -90,7 +90,7 @@ pip install black pre-commit
 conda -c conda-forge black pre-commit
 ```
 
-2. Navigate to your local copy of the casanovo repository and activate the hook:
+2. Navigate to your local copy of the Casanovo repository and activate the hook:
 ```bash
 pre-commit install
 ```

README.md

@@ -52,7 +52,7 @@ The base environment most likely will not work.
 Install Casanovo as a Python package from this repository (requires 3.8 ≥ [Python version] > 3.10 , dependencies will be installed automatically as needed):
 
 ```
-pip install git+https://github.com/Noble-Lab/casanovo.git#egg=casanovo
+pip install casanovo
 ```
 
 Once installed, Casanovo can be used with a simple command line interface.

casanovo/casanovo.py

@@ -163,8 +163,10 @@ def main(
     }
     # Add extra configuration options and scale by the number of GPUs.
     n_gpus = torch.cuda.device_count()
-    config["n_workers"] = len(psutil.Process().cpu_affinity()) // n_gpus
-    config["train_batch_size"] = config["train_batch_size"] // n_gpus
+    config["n_workers"] = len(psutil.Process().cpu_affinity())
+    if n_gpus > 1:
+        config["n_workers"] = config["n_workers"] // n_gpus
+        config["train_batch_size"] = config["train_batch_size"] // n_gpus
 
     pl.utilities.seed.seed_everything(seed=config["random_seed"], workers=True)
 

casanovo/denovo/model.py

@@ -8,7 +8,6 @@
 import pytorch_lightning as pl
 import torch
 from depthcharge.components import ModelMixin, PeptideDecoder, SpectrumEncoder
-from depthcharge.models.embed.model import PairedSpectrumEncoder
 
 from . import evaluate
 from ..data import ms_io
@@ -85,9 +84,7 @@ def __init__(
         n_layers: int = 1,
         dropout: float = 0.0,
         dim_intensity: Optional[int] = None,
-        custom_encoder: Optional[
-            Union[SpectrumEncoder, PairedSpectrumEncoder]
-        ] = None,
+        custom_encoder: Optional[SpectrumEncoder] = None,
         max_length: int = 100,
         residues: Union[Dict[str, float], str] = "canonical",
         max_charge: int = 5,
@@ -106,10 +103,7 @@ def __init__(
 
         # Build the model.
         if custom_encoder is not None:
-            if isinstance(custom_encoder, PairedSpectrumEncoder):
-                self.encoder = custom_encoder.encoder
-            else:
-                self.encoder = custom_encoder
+            self.encoder = custom_encoder
         else:
             self.encoder = SpectrumEncoder(
                 dim_model=dim_model,

setup.cfg

@@ -1,5 +1,5 @@
 [metadata]
-name = Casanovo
+name = casanovo
 author = Melih Yilmaz
 author_email = melih@cs.washington.edu
 description = De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
@@ -22,7 +22,7 @@ packages = find:
 python_requires = >=3.8
 install_requires =
     click
-    depthcharge-ms @ git+https://github.com/wfondrie/depthcharge@3dda29053ab479fa31fa1309f65f285d04481c1e
+    depthcharge-ms>=0.0.1
     numpy
     pandas
     psutil

tests/conftest.py

@@ -1,25 +1,9 @@
-"""Fixtures used for testing
-
-We need:
-- To set the PPX_DATA_DIR environment variable to a temporary directory
-- A mock GET response from PRIDE
-- A mock GET response from ProteomeXchange
-- A mock FTP server response from PRIDE
-- A mock FTP server response from MassIVE
-"""
-import json
-import socket
-import ftplib
-
+"""Setup tests for casanovo"""
 import pytest
-import requests
-import ppx
 
 from pyteomics.mass import calculate_mass
 import numpy as np
 
-# Pytest fixtures added here can be used as parameters for testing methods
-
 
 @pytest.fixture
 def mgf_small(tmp_path):
@@ -29,7 +13,6 @@ def mgf_small(tmp_path):
     return _create_mgf(peptides, mgf_file)
 
 
-# Utility Funcs
 def _create_mgf(peptides, mgf_file, random_state=42):
     """Create a fake MGF file from one or more peptides.
     Parameters
@@ -90,117 +73,3 @@ def _create_mgf_entry(peptide, charge=2):
         "END IONS",
     ]
     return "\n".join(mgf)
-
-
-# Set the PPX_DATA_DIRECTORY --------------------------------------------------
-@pytest.fixture(autouse=True)
-def ppx_data_dir(monkeypatch, tmp_path):
-    """Set the PPX_DATA_DIR environment variable"""
-    monkeypatch.setenv("PPX_DATA_DIR", str(tmp_path))
-    ppx.set_data_dir()
-
-
-# PRIDE projects/<accession>/files endpoint -----------------------------------
-class MockPrideFilesResponse:
-    """A mock of the PRIDE files REST response"""
-
-    status_code = 200
-
-    @staticmethod
-    def json():
-        with open("tests/data/pride_files_response.json") as ref:
-            out = json.load(ref)
-
-        return out
-
-
-@pytest.fixture
-def mock_pride_files_response(monkeypatch):
-    """Patch requests.get() to use a local file."""
-
-    def mock_get(*args, **kwargs):
-        return MockPrideFilesResponse()
-
-    monkeypatch.setattr(requests, "get", mock_get)
-
-
-# PRIDE projects/<accession? endpoint -----------------------------------------
-class MockPrideProjectResponse:
-    """A mock of the PRIDE projects REST response"""
-
-    status_code = 200
-
-    @staticmethod
-    def json():
-        with open("tests/data/pride_project_response.json") as ref:
-            out = json.load(ref)
-
-        return out
-
-
-@pytest.fixture
-def mock_pride_project_response(monkeypatch):
-    """Patch requests.get() to use a local file."""
-
-    def mock_get(*args, **kwargs):
-        return MockPrideProjectResponse()
-
-    monkeypatch.setattr(requests, "get", mock_get)
-
-
-# MassIVE FTP server ----------------------------------------------------------
-class MockMassiveFtpResponse:
-    """A mock of the MassIVE FTP server response"""
-
-    @staticmethod
-    def dir(fun):
-        with open("tests/data/massive_ftp_response.txt") as ref:
-            [fun(line) for line in ref]
-
-
-def mock_massive_ftp_response(monkeypatch):
-    """Patch ftplib to use a local file as a response"""
-
-    def null(*args, **kwargs):
-        pass
-
-    def mock_dir(fun):
-        with open("tests/data/massive_ftp_response.txt") as ref:
-            [fun(line) for line in ref]
-
-    monkeypatch.setattr(ftplib.FTP, "login", null)
-    monkeypatch.setattr(ftplib.FTP, "cwd", null)
-    monkeypatch.setattr(ftplib.FTP, "dir", mock_dir)
-
-
-# Mock up local files ---------------------------------------------------------
-@pytest.fixture
-def local_files(tmp_path):
-    """Create some files to test local file detection"""
-    local_dirs = [tmp_path / f"test_dir{i}" for i in range(10)]
-    local_files = []
-    for local_dir in local_dirs:
-        local_dir.mkdir()
-        files = [
-            local_dir / "test_file.mzML",
-            local_dir / "test_file.txt",
-        ]
-        local_files += files
-        for local_file in files:
-            local_file.touch()
-
-    local_files.append(tmp_path / "test_file.mzML")
-    local_files[-1].touch()
-    return local_files, local_dirs
-
-
-# Block internet --------------------------------------------------------------
-@pytest.fixture
-def block_internet(monkeypatch):
-    """Turn off internet access"""
-
-    class Blocker(socket.socket):
-        def __init__(self, *args, **kwargs):
-            raise OSError("Network call blocked")
-
-    monkeypatch.setattr(socket, "socket", Blocker)