Add sys_info utility to display dependencies version (#122)

* add sys_info utility

* fix import

* fix style

.github/workflows/build.yml

@@ -37,20 +37,20 @@ jobs:
           python -m pip install --progress-bar off --upgrade pip setuptools wheel
           python -m pip install --progress-bar off .[build]
       - name: Test package install
-        run: python -c "import pycrostates; print(pycrostates.__version__)"
+        run: pycrostates-sys_info
       - name: Remove package install
         run: python -m pip uninstall -y pycrostates
       - name: Build package
         run: python -m build
       - name: Install sdist
         run: pip install ./dist/*.tar.gz
       - name: Test sdist install
-        run: python -c "import pycrostates; print(pycrostates.__version__)"
+        run: pycrostates-sys_info
       - name: Remove sdist install
         run: python -m pip uninstall -y pycrostates
       - name: Install wheel
         run: pip install ./dist/*.whl
       - name: Test wheel install
-        run: python -c "import pycrostates; print(pycrostates.__version__)"
+        run: pycrostates-sys_info
       - name: Remove wheel install
         run: python -m pip uninstall -y pycrostates

azure-pipelines.yml

@@ -128,6 +128,8 @@ stages:
         python -m pip install --progress-bar off --upgrade --pre --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --timeout=180 numpy scipy scikit-learn matplotlib
       condition: eq(variables.PRE, 'true')
       displayName: 'Install pre-release dependencies'
+    - script: pycrostates-sys_info --developer
+      displayName: 'Display Pycrostates config'
     - script: mne sys_info -pd
       displayName: 'Display MNE config'
     - script: |

pycrostates/__init__.py

@@ -3,6 +3,7 @@
 from . import cluster, datasets, metrics, preprocessing, utils, viz
 from ._version import __version__  # noqa: F401
 from .utils._logs import set_log_level
+from .utils.sys_info import sys_info  # noqa: F401
 
 __all__ = (
     "cluster",
@@ -12,4 +13,5 @@
     "utils",
     "viz",
     "set_log_level",
+    "sys_info",
 )

pycrostates/commands/sys_info.py

@@ -0,0 +1,18 @@
+import argparse
+
+from .. import sys_info
+
+
+def run():
+    """Run sys_info() command."""
+    parser = argparse.ArgumentParser(
+        prog=f"{__package__.split('.')[0]}-sys_info", description="sys_info"
+    )
+    parser.add_argument(
+        "--developer",
+        help="display information for optional dependencies",
+        action="store_true",
+    )
+    args = parser.parse_args()
+
+    sys_info(developer=args.developer)

pycrostates/utils/sys_info.py

@@ -0,0 +1,121 @@
+import platform
+import sys
+from functools import partial
+from importlib.metadata import requires, version
+from typing import IO, Callable, List, Optional
+
+import psutil
+from packaging.requirements import Requirement
+
+from ._checks import _check_type
+
+
+def sys_info(fid: Optional[IO] = None, developer: bool = False):
+    """Print the system information for debugging.
+
+    Parameters
+    ----------
+    fid : file-like | None
+        The file to write to, passed to :func:`print`. Can be None to use
+        :data:`sys.stdout`.
+    developer : bool
+        If True, display information about optional dependencies.
+    """
+    _check_type(developer, (bool,), "developer")
+
+    ljust = 26
+    out = partial(print, end="", file=fid)
+    package = __package__.split(".")[0]
+
+    # OS information - requires python 3.8 or above
+    out("Platform:".ljust(ljust) + platform.platform() + "\n")
+    # python information
+    out("Python:".ljust(ljust) + sys.version.replace("\n", " ") + "\n")
+    out("Executable:".ljust(ljust) + sys.executable + "\n")
+    # CPU information
+    out("CPU:".ljust(ljust) + platform.processor() + "\n")
+    out("Physical cores:".ljust(ljust) + str(psutil.cpu_count(False)) + "\n")
+    out("Logical cores:".ljust(ljust) + str(psutil.cpu_count(True)) + "\n")
+    # memory information
+    out("RAM:".ljust(ljust))
+    out(f"{psutil.virtual_memory().total / float(2 ** 30):0.1f} GB\n")
+    out("SWAP:".ljust(ljust))
+    out(f"{psutil.swap_memory().total / float(2 ** 30):0.1f} GB\n")
+    # package information
+    out(f"{package}:".ljust(ljust) + version(package) + "\n")
+
+    # dependencies
+    out("\nCore dependencies\n")
+    dependencies = [Requirement(elt) for elt in requires(package)]
+    core_dependencies = [dep for dep in dependencies if "extra" not in str(dep.marker)]
+    _list_dependencies_info(out, ljust, package, core_dependencies)
+
+    # extras
+    if developer:
+        keys = (
+            "build",
+            "docs",
+            "test",
+            "style",
+        )
+        for key in keys:
+            extra_dependencies = [
+                dep
+                for dep in dependencies
+                if all(elt in str(dep.marker) for elt in ("extra", key))
+            ]
+            if len(extra_dependencies) == 0:
+                continue
+            out(f"\nOptional '{key}' dependencies\n")
+            _list_dependencies_info(out, ljust, package, extra_dependencies)
+
+
+def _list_dependencies_info(
+    out: Callable, ljust: int, package: str, dependencies: List[Requirement]
+):
+    """List dependencies names and versions."""
+    unicode = sys.stdout.encoding.lower().startswith("utf")
+    if unicode:
+        ljust += 1
+
+    not_found: List[Requirement] = list()
+    for dep in dependencies:
+        if dep.name == package:
+            continue
+        try:
+            version_ = version(dep.name)
+        except Exception:
+            not_found.append(dep)
+            continue
+
+        # build the output string step by step
+        output = f"✔︎ {dep.name}" if unicode else dep.name
+        # handle version specifiers
+        if len(dep.specifier) != 0:
+            output += f" ({str(dep.specifier)})"
+        output += ":"
+        output = output.ljust(ljust) + version_
+
+        # handle special dependencies with backends, C dep, ..
+        if dep.name in ("matplotlib", "seaborn") and version_ != "Not found.":
+            try:
+                from matplotlib import pyplot as plt
+
+                backend = plt.get_backend()
+            except Exception:
+                backend = "Not found"
+
+            output += f" (backend: {backend})"
+        out(output + "\n")
+
+    if len(not_found) != 0:
+        not_found = [
+            f"{dep.name} ({str(dep.specifier)})"
+            if len(dep.specifier) != 0
+            else dep.name
+            for dep in not_found
+        ]
+        if unicode:
+            out(f"✘ Not installed: {', '.join(not_found)}\n")
+        else:
+            out(f"Not installed: {', '.join(not_found)}\n")

pycrostates/utils/tests/test_sys_info.py

@@ -0,0 +1,36 @@
+"""Test config.py"""
+
+from io import StringIO
+
+from pycrostates.utils.sys_info import sys_info
+
+
+def test_sys_info():
+    """Test info-showing utility."""
+    out = StringIO()
+    sys_info(fid=out)
+    value = out.getvalue()
+    out.close()
+    assert "Platform:" in value
+    assert "Executable:" in value
+    assert "CPU:" in value
+    assert "Physical cores:" in value
+    assert "Logical cores" in value
+    assert "RAM:" in value
+    assert "SWAP:" in value
+
+    assert "numpy" in value
+    assert "psutil" in value
+
+    assert "style" not in value
+    assert "test" not in value
+
+    out = StringIO()
+    sys_info(fid=out, developer=True)
+    value = out.getvalue()
+    out.close()
+
+    assert "build" in value
+    assert "docs" in value
+    assert "style" in value
+    assert "test" in value

pyproject.toml

@@ -47,7 +47,9 @@ dependencies = [
     'matplotlib',
     'mne>=1.2',
     'numpy>=1.21',
+    'packaging',
     'pooch',
+    'psutil',
     'scikit-learn',
     'scipy',
 ]
@@ -95,6 +97,9 @@ documentation = 'https://pycrostates.readthedocs.io/en/master/'
 source = 'https://github.com/vferat/pycrostates'
 tracker = 'https://github.com/vferat/pycrostates/issues'
 
+[project.scripts]
+pycrostates-sys_info = 'pycrostates.commands.sys_info:run'
+
 [tool.setuptools]
 include-package-data = false