switch to pyproject, modernize everything (#159)

.github/workflows/ci.yaml

@@ -8,38 +8,43 @@ on:
         - cron:  '5 0 * * *'
 
 jobs:
-    flake8:
-        runs-on: ubuntu-latest
-        steps:
-        - uses: actions/checkout@v4
-        - name: Set up Python
-          uses: actions/setup-python@v4
-          with:
-            # matches compat target in setup.py
-            python-version: '3.7'
-        - name: Run flake8
-          run: |
-            pip install -U flake8 pep8-naming flake8-quotes flake8-comprehensions flake8-isort types-psutil numpy flake8-bugbear
-            flake8 setup.py doc/conf.py logpyle bin/* examples/*.py test/*.py
+    ruff:
+      runs-on: ubuntu-latest
+      steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+      - name: Ruff check
+        run: |
+          python -m pip install ruff
+          ruff check
+
+    typos:
+      runs-on: ubuntu-latest
+      steps:
+      - uses: actions/checkout@v4
+      - uses: crate-ci/typos@master
 
     examples:
         runs-on: ${{ matrix.os }}
         strategy:
           fail-fast: true
           matrix:
-            python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12', '3.x']
-            os: [ubuntu-latest, macos-13]
+            python-version: ['3.10', '3.11', '3.12', '3.13', '3.x']
+            os: [ubuntu-latest, macos-latest]
 
         steps:
         - uses: actions/checkout@v4
         - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
-          uses: actions/setup-python@v4
+          uses: actions/setup-python@v5
           with:
             python-version: ${{ matrix.python-version }}
         - name: Install prerequisites
           run: |
             [[ $(uname) == "Darwin" ]] && brew install open-mpi
-            [[ $(uname) == "Linux" ]] && sudo apt-get update && sudo apt-get install -y mpich libmpich-dev
+            [[ $(uname) == "Linux" ]] && sudo apt-get update && sudo apt-get install -y libopenmpi-dev
             pip install wheel matplotlib mpi4py psutil
             pip install -e .
         - name: Run and test examples
@@ -53,7 +58,7 @@ jobs:
 
             ## Check for warnings and logging
             runalyzer summary.sqlite  -c 'db.print_cursor(db.q("select * from warnings"))'
-            runalyzer summary.sqlite  -c 'db.print_cursor(db.q("select * from warnings"))' | grep Oof
+            runalyzer summary.sqlite  -c 'db.print_cursor(db.q("select * from warnings"))' | grep "warnings capture test"
             runalyzer summary.sqlite  -c 'db.print_cursor(db.q("select * from logging"))'
             runalyzer summary.sqlite  -c 'db.print_cursor(db.q("select * from logging"))' | grep WARNING
 
@@ -89,7 +94,7 @@ jobs:
 
             ## Check for warnings and logging
             runalyzer summary.sqlite  -c 'db.print_cursor(db.q("select * from warnings"))'
-            runalyzer summary.sqlite  -c 'db.print_cursor(db.q("select * from warnings"))' | grep Oof
+            runalyzer summary.sqlite  -c 'db.print_cursor(db.q("select * from warnings"))' | grep "warnings capture test"
             runalyzer summary.sqlite  -c 'db.print_cursor(db.q("select * from logging"))'
             runalyzer summary.sqlite  -c 'db.print_cursor(db.q("select * from logging"))' | grep WARNING
 
@@ -151,7 +156,7 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: actions/setup-python@v4
+        - uses: actions/setup-python@v5
           with:
             python-version: '3.x'
         - name: "Main Script"
@@ -165,20 +170,22 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: actions/setup-python@v4
+        - uses: actions/setup-python@v5
           with:
             python-version: '3.x'
         - name: "Main Script"
           run: |
+            set -x
+            sudo apt-get update && sudo apt-get install -y libopenmpi-dev
             curl -L -O -k https://gitlab.tiker.net/inducer/ci-support/raw/main/prepare-and-run-mypy.sh
-            export EXTRA_INSTALL="pytools numpy types-psutil pymbolic"
+            export EXTRA_INSTALL="pytools numpy types-psutil pymbolic mpi4py matplotlib"
             . ./prepare-and-run-mypy.sh python3
 
     pytest:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: actions/setup-python@v4
+        - uses: actions/setup-python@v5
           with:
             python-version: '3.x'
 
@@ -196,7 +203,7 @@ jobs:
       runs-on: ubuntu-latest
       steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.x'
       - name: Compare coverage with 'main' branch
@@ -226,7 +233,7 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: actions/setup-python@v4
+        - uses: actions/setup-python@v5
           with:
             python-version: '3.x'
 
@@ -245,7 +252,7 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: actions/setup-python@v4
+        - uses: actions/setup-python@v5
           with:
             python-version: '3.x'
 

doc/analysis.rst

@@ -32,7 +32,7 @@ the hood, this ensures that the quantity is gathered from all present run_ids.
 
 Magic refers to the usage of customized commands to operate on our mangled and
 non-mangled SQL queries. To issue a magic command, preceding it with a ``.``.
-This will issue a command to runalyzer instead of refering to a python symbol.
+This will issue a command to runalyzer instead of referring to a python symbol.
 
 Running the script
 ------------------
@@ -222,11 +222,11 @@ before serving it.
 Usage
 -----
 After the virtual environment has been setup, click the ``Add file`` button
-to add a pannel for analysis.
+to add a panel for analysis.
 
 To analyze a run, click on the browse button to upload one or more files.
 These files will be gathered together under the hood. You can then select
-quantites from the X and Y dropdowns. If you would like to keep track of
+quantities from the X and Y dropdowns. If you would like to keep track of
 multiple quantities in the same graph, you can press ``Add Line to Plot``
 to add a Y dropdown.
 

doc/conf.py

@@ -1,99 +1,32 @@
 #!/usr/bin/env python3
 
-import sys
+from urllib.request import urlopen
 
-# -- General configuration ------------------------------------------------
+from logpyle import __version__
 
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
+# {{{ linkcode_resolve
 
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = [
-    "sphinx.ext.autodoc",
-    "sphinx.ext.doctest",
-    "sphinx.ext.intersphinx",
-    "sphinx.ext.mathjax",
-    "sphinx.ext.todo",
-    "sphinx.ext.viewcode",
-    "sphinx.ext.napoleon",
-    "sphinx_copybutton",
-]
-autoclass_content = "class"
-# autodoc_typehints = "description"
+_conf_url = \
+    "https://raw.githubusercontent.com/inducer/sphinxconfig/main/sphinxconfig.py"
+with urlopen(_conf_url) as _inf:
+    exec(compile(_inf.read(), _conf_url, "exec"), globals())
 
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ["_templates"]
+old_linkcode_resolve = linkcode_resolve  # noqa: F821 (linkcode_resolve comes from the URL above)
 
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
-source_suffix = ".rst"
 
-# The master toctree document.
-master_doc = "index"
+def linkcode_resolve(*args, **kwargs):
+    linkcode_url = "https://github.com/illinois-ceesd/logpyle/blob/main/{filepath}#L{linestart}-L{linestop}"
+    return old_linkcode_resolve(*args, **kwargs, linkcode_url=linkcode_url)
+
+
+# }}}
 
 # General information about the project.
 project = "logpyle"
 copyright = "2017, Andreas Kloeckner"
 author = "Andreas Kloeckner"
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-ver_dic = {}
-exec(
-    compile(open("../logpyle/version.py").read(), "../logpyle/version.py", "exec"),
-    ver_dic,
-)
-version = ".".join(str(x) for x in ver_dic["VERSION"])
-release = ver_dic["VERSION_TEXT"]
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = "en"
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = "sphinx"
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = True
-
-nitpicky = True
-
-
-# -- Options for HTML output ----------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = "furo"
-
-html_theme_options = {}
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further.  For a list of options available for each theme, see the
-# documentation.
-#
-# html_theme_options = {}
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-# html_static_path = ['_static']
+version = __version__
+release = __version__
 
 
 intersphinx_mapping = {
@@ -103,6 +36,3 @@
     "pytools": ("https://documen.tician.de/pytools/", None),
     "mpi4py": ("https://mpi4py.readthedocs.io/en/stable/", None),
 }
-
-
-sys._BUILDING_SPHINX_DOCS = True

examples/log-mpi.py

@@ -1,15 +1,23 @@
 #!/usr/bin/env python3
 
 import logging
+from collections.abc import Callable
 from random import uniform
 from time import sleep
-from typing import Any, Callable
+from typing import Any
 from warnings import warn
 
 from mpi4py import MPI
 
-from logpyle import (IntervalTimer, LogManager, LogQuantity, add_general_quantities,
-                     add_run_info, add_simulation_quantities, set_dt)
+from logpyle import (
+    IntervalTimer,
+    LogManager,
+    LogQuantity,
+    add_general_quantities,
+    add_run_info,
+    add_simulation_quantities,
+    set_dt,
+)
 
 
 class Fifteen(LogQuantity):
@@ -68,7 +76,7 @@ def main() -> None:
 
         # Illustrate warnings/logging capture
         if uniform(0, 1) < 0.05:
-            warn("Oof. Something went awry.")
+            warn("warnings capture test", stacklevel=2)
 
         if istep == 16:
             logger.warning("test logging")

examples/log.py

@@ -5,9 +5,16 @@
 from time import sleep
 from warnings import warn
 
-from logpyle import (GCStats, IntervalTimer, LogManager, LogQuantity,
-                     add_general_quantities, add_run_info, add_simulation_quantities,
-                     set_dt)
+from logpyle import (
+    GCStats,
+    IntervalTimer,
+    LogManager,
+    LogQuantity,
+    add_general_quantities,
+    add_run_info,
+    add_simulation_quantities,
+    set_dt,
+)
 
 
 class Fifteen(LogQuantity):
@@ -59,7 +66,7 @@ def main() -> None:
 
         # Illustrate warnings capture
         if uniform(0, 1) < 0.05:
-            warn("Oof. Something went awry.")
+            warn("warnings capture test", stacklevel=2)
 
         if istep == 50:
             logger.warning("test logging")

examples/optional-log.py

@@ -3,13 +3,19 @@
 from contextlib import nullcontext
 from random import uniform
 from time import sleep
-from typing import Union
 
-from logpyle import (IntervalTimer, LogManager, _SubTimer, add_general_quantities,
-                     add_run_info, add_simulation_quantities, set_dt)
+from logpyle import (
+    IntervalTimer,
+    LogManager,
+    _SubTimer,
+    add_general_quantities,
+    add_run_info,
+    add_simulation_quantities,
+    set_dt,
+)
 
 
-def main(use_logpyle: bool) -> None:
+def main(use_logpyle: bool) -> None:  # noqa: C901
     if use_logpyle:
         logmgr = LogManager("optional-log.sqlite", "w")
     else:
@@ -25,7 +31,7 @@ def main(use_logpyle: bool) -> None:
     if logmgr:
         vis_timer = IntervalTimer("t_vis", "Time spent visualizing")
         logmgr.add_quantity(vis_timer)
-        time_vis: Union[_SubTimer, nullcontext[None]] = vis_timer.get_sub_timer()
+        time_vis: _SubTimer | nullcontext[None] = vis_timer.get_sub_timer()
     else:
         time_vis = nullcontext()