Merge pull request #361 from glotzerlab/reproducible-doc-builds

Use a reproducible configuration to build docs.

.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.12"
 
 sphinx:
   fail_on_warning: true

.ruff.toml

@@ -1,6 +1,6 @@
 target-version = "py38"
 
-extend-select = [
+lint.extend-select = [
     "A",
     "B",
     "D",
@@ -19,7 +19,7 @@ extend-select = [
     "W",
 ]
 
-ignore = [
+lint.ignore = [
   "N806", "N803",  # Allow occasional use of uppercase variable and argument names (e.g. N).
   "D107", # Do not document __init__ separately from the class.
   "PLR09", # Allow "too many" statements/arguments/etc...
@@ -40,7 +40,7 @@ ignore = [
                  "D", # conf.py does not need documentation
     ]
 
-[pydocstyle]
+[lint.pydocstyle]
 convention = "google"
 
 [format]

doc/requirements.in

@@ -0,0 +1,8 @@
+breathe == 4.35.0
+cython == 3.0.10
+furo == 2024.1.29
+ipython == 8.23.0
+numpy == 1.26.4
+pandas == 2.2.2
+pyarrow == 16.0.0
+sphinx == 7.3.7

doc/requirements.txt

@@ -1,8 +1,118 @@
-breathe == 4.35.0
-cython == 3.0.10
-furo == 2024.1.29
-ipython == 8.23.0
-numpy == 1.26.4
-pandas == 2.2.1
-pyarrow == 15.0.2
-sphinx
+#
+# This file is autogenerated by pip-compile with Python 3.12
+# by the following command:
+#
+#    pip-compile requirements.in
+#
+alabaster==0.7.16
+    # via sphinx
+asttokens==2.4.1
+    # via stack-data
+babel==2.14.0
+    # via sphinx
+beautifulsoup4==4.12.3
+    # via furo
+breathe==4.35.0
+    # via -r requirements.in
+certifi==2024.2.2
+    # via requests
+charset-normalizer==3.3.2
+    # via requests
+cython==3.0.10
+    # via -r requirements.in
+decorator==5.1.1
+    # via ipython
+docutils==0.21.2
+    # via
+    #   breathe
+    #   sphinx
+executing==2.0.1
+    # via stack-data
+furo==2024.1.29
+    # via -r requirements.in
+idna==3.7
+    # via requests
+imagesize==1.4.1
+    # via sphinx
+ipython==8.23.0
+    # via -r requirements.in
+jedi==0.19.1
+    # via ipython
+jinja2==3.1.3
+    # via sphinx
+markupsafe==2.1.5
+    # via jinja2
+matplotlib-inline==0.1.7
+    # via ipython
+numpy==1.26.4
+    # via
+    #   -r requirements.in
+    #   pandas
+    #   pyarrow
+packaging==24.0
+    # via sphinx
+pandas==2.2.2
+    # via -r requirements.in
+parso==0.8.4
+    # via jedi
+pexpect==4.9.0
+    # via ipython
+prompt-toolkit==3.0.43
+    # via ipython
+ptyprocess==0.7.0
+    # via pexpect
+pure-eval==0.2.2
+    # via stack-data
+pyarrow==16.0.0
+    # via -r requirements.in
+pygments==2.17.2
+    # via
+    #   furo
+    #   ipython
+    #   sphinx
+python-dateutil==2.9.0.post0
+    # via pandas
+pytz==2024.1
+    # via pandas
+requests==2.31.0
+    # via sphinx
+six==1.16.0
+    # via
+    #   asttokens
+    #   python-dateutil
+snowballstemmer==2.2.0
+    # via sphinx
+soupsieve==2.5
+    # via beautifulsoup4
+sphinx==7.3.7
+    # via
+    #   -r requirements.in
+    #   breathe
+    #   furo
+    #   sphinx-basic-ng
+sphinx-basic-ng==1.0.0b2
+    # via furo
+sphinxcontrib-applehelp==1.0.8
+    # via sphinx
+sphinxcontrib-devhelp==1.0.6
+    # via sphinx
+sphinxcontrib-htmlhelp==2.0.5
+    # via sphinx
+sphinxcontrib-jsmath==1.0.1
+    # via sphinx
+sphinxcontrib-qthelp==1.0.7
+    # via sphinx
+sphinxcontrib-serializinghtml==1.1.10
+    # via sphinx
+stack-data==0.6.3
+    # via ipython
+traitlets==5.14.3
+    # via
+    #   ipython
+    #   matplotlib-inline
+tzdata==2024.1
+    # via pandas
+urllib3==2.2.1
+    # via requests
+wcwidth==0.2.13
+    # via prompt-toolkit

gsd/test/test_fl.py

@@ -405,9 +405,8 @@ def test_dtype_errors(tmp_path, open_mode):
 
 def test_truncate(tmp_path):
     """Test that the truncate method functions."""
-    data = numpy.ascontiguousarray(
-        numpy.random.random(size=(1000, 3)), dtype=numpy.float32
-    )
+    rng = numpy.random.default_rng()
+    data = numpy.ascontiguousarray(rng.random(size=(1000, 3)), dtype=numpy.float32)
     with gsd.fl.open(
         name=tmp_path / 'test_truncate.gsd',
         mode='w',

scripts/benchmark-hoomd.py

@@ -101,8 +101,9 @@ def run_benchmarks(N, size):
     bmark_read_size = 0.25 * 1024**3
 
     timings = {}
-    position = numpy.random.random((N, 3)).astype('float32')
-    orientation = numpy.random.random((N, 4)).astype('float32')
+    rng = numpy.random.default_rng()
+    position = rng.random((N, 3)).astype('float32')
+    orientation = rng.random((N, 4)).astype('float32')
 
     nframes = compute_nframes(N, size)
     actual_size = compute_actual_size(N, nframes)