Add support for Windows (#151)

Add support for Windows:

- [x] Make extra compile arguments compatible
- [x] Add Windows to build platforms in cibuildwheel action
- [x] Update readme

Extra:
- [x] Made `HCD` model name synonymous to `HCD2021` for backwards compatibility
- [x] Fixed build for macOS: Missing XGBoost dependency in build environment: `libomp`
- [x] Avoid extra test runs due to `on: [push, pull_request]` by specifying push branch

Caveats for compiled wheels: 
- 32bit platforms not built, as XGBoost wheels are missing
- Python 3.9 and 3.10 not built, as pyTables wheels are missing: PyTables/PyTables#823

.github/workflows/build_and_publish.yml

@@ -15,11 +15,11 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: '3.9'
+          python-version: '3.10'
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools numpy cython flake8
+          pip install setuptools oldest-supported-numpy cython flake8
       - name: Check for syntax errors
         run: |
           flake8 ./ms2pip ./fasta2speclib --count --select=E9,F63,F7,F82 --show-source --statistics
@@ -35,25 +35,28 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-18.04, macos-latest]
+        os: [ubuntu-18.04, windows-latest, macos-latest]
     steps:
       - uses: actions/checkout@v2
         with:
           lfs: 'true'
       - uses: actions/setup-python@v2
         name: Install Python
         with:
-          python-version: '3.7'
+          python-version: '3.10'
       - name: Check for syntax errors
         run: |
           pip install flake8
           flake8 ./ms2pip ./fasta2speclib --count --select=E9,F63,F7,F82 --show-source --statistics
-      - uses: joerick/cibuildwheel@v1.7.4
+      - uses: joerick/cibuildwheel@v2.2.2
         with:
           output-dir: dist
         env:
-          CIBW_BUILD: "cp3*-macosx_x86_64 cp3*-manylinux_x86_64"
-          CIBW_SKIP: "cp35-* cp39-macosx_x86_64" # see compomics/ms2pip_c#126
+          # No XGBoost wheels for 32bit Windows
+          # No PyTables wheels for Python 3.9 and 3.10 yet; see compomics/ms2pip_c#126
+          CIBW_BUILD: "cp3*-manylinux_x86_64 cp3*-win_amd64 cp3*-macosx_x86_64"
+          CIBW_SKIP: "cp39-* cp310-*"
+          CIBW_BEFORE_ALL_MACOS: "brew install libomp"
           CIBW_MANYLINUX_X86_64_IMAGE: "manylinux2014"
           CIBW_TEST_REQUIRES: "pytest"
           CIBW_TEST_COMMAND: "pytest {project}/tests"

.github/workflows/test.yml

@@ -1,6 +1,10 @@
 name: Tests
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - releases
+  pull_request:
 
 jobs:
   build:
@@ -9,7 +13,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.6, 3.7, 3.8]
 
     steps:
     - uses: actions/checkout@v2

README.md

@@ -76,6 +76,11 @@ With Python 3.6 or higher, run:
 pip install ms2pip
 ```
 
+Compiled wheels are available for Python 3.6, 3.7, and 3.8, on 64bit Linux,
+Windows, and macOS. This should install MS²PIP in a few seconds. For other
+platforms, MS²PIP can be built from source, although it can take up to one hour
+to compile the large prediction models.
+
 We recommend using a [venv](https://docs.python.org/3/library/venv.html) or
 [conda](https://docs.conda.io/en/latest/) virtual environment.
 
@@ -86,6 +91,8 @@ Install with activated bioconda and conda-forge channels:
 conda install -c defaults -c bioconda -c conda-forge ms2pip
 ```
 
+Bioconda packages are only available for Linux and macOS.
+
 #### Docker container
 First check the latest version tag on [biocontainers/ms2pip/tags](https://quay.io/repository/biocontainers/ms2pip?tab=tags). Then pull and run the container with
 ```

ms2pip/ms2pipC.py

@@ -120,6 +120,7 @@
         }
     },
 }
+MODELS["HCD"] = MODELS["HCD2021"]
 
 
 def process_peptides(worker_num, data, afile, modfile, modfile2, PTMmap, model):

setup.py

@@ -1,4 +1,5 @@
 import os
+import platform
 from glob import glob
 
 from setuptools import setup
@@ -67,17 +68,32 @@
 ]
 #_ = [[os.remove(f) for f in glob(pat)] for pat in to_remove]
 
+# Large machine-written C model files require optimization to be disabled
+compile_args = {
+    "Linux": [
+        "-O0",
+        "-fno-var-tracking",
+        "-Wno-unused-result",
+        "-Wno-cpp",
+        "-Wno-unused-function",
+    ],
+    "Darwin": [
+        "-O0",
+    ],
+    "Windows": [    
+        "/Od",
+        "/DEBUG",
+        "/GL-",
+        "/bigobj",
+        "/wd4244",
+    ]
+}
+
 extensions = [
     Extension(
         "ms2pip.cython_modules.ms2pip_pyx",
         sources=["ms2pip/cython_modules/ms2pip_pyx.pyx"] + glob("ms2pip/models/*/*.c"),
-        extra_compile_args=[
-            "-fno-var-tracking",
-            "-Og",
-            "-Wno-unused-result",
-            "-Wno-cpp",
-            "-Wno-unused-function",
-        ],
+        extra_compile_args=compile_args[platform.system()],
     )
 ]