Release 3.0.2 (PR #199)

.github/workflows/tests.yml

@@ -0,0 +1,88 @@
+name: tests
+
+on:
+  push:
+    branches:
+      - develop
+      - master
+  pull_request:
+    branches:
+      - develop
+      - master
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8"]
+    env:
+      PYTHON: ${{ matrix.python-version }}
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install poetry
+        run: pip install poetry
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'poetry'
+      - name: Install mdbenchmark
+        run: poetry install --extras docs
+      - name: Check reformat
+        run: poetry run make reformat-check
+      - name: Check style
+        run: poetry run make flake8
+      - name: Check sort
+        run: poetry run make isort-check
+      - name: Check reStructuredText
+        run: poetry run make rst-lint
+      - name: Unit-tests
+        run: poetry run pytest -v --cov=mdbenchmark --cov-report=xml
+      - name: Upload coverage
+        uses: codecov/codecov-action@v3
+        with:
+          env_vars: PYTHON
+          fail_ci_if_error: true
+      - name: Build distribution
+        run: poetry build
+      - name: Upload build artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: dists.${{ matrix.python-version }}
+          path: dist/
+      - name: Make docs
+        run: |
+          cd docs
+          poetry run make build
+
+  test-build:
+
+    runs-on: ubuntu-latest
+    needs: test
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8"]
+
+    steps:
+      - name: Enable pip-caching
+        run: touch requirements.txt
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip' #doesn't seem to work
+      - name: Update pip
+        run: pip install --upgrade pip
+      - name: Download build artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: dists.${{ matrix.python-version }}
+          path: dist
+      - name: Install mdbenchmark
+        run: pip install dist/*.tar.gz
+      - name: Check run
+        run: mdbenchmark
+

CHANGELOG.rst

@@ -1,3 +1,22 @@
+3.0.2 (2023-02-20)
+==================
+
+Features
+--------
+
+- Moved from travis to github-actions (PR 181) (`#181 <https://github.com/bio-phys/MDBenchmark/issues/181>`_)
+- Add test to CI to verify distribution with pip. (PR 182) (`#182 <https://github.com/bio-phys/MDBenchmark/issues/182>`_)
+- Make scaling projection show optimal scaling. (PR 193) (`#193 <https://github.com/bio-phys/MDBenchmark/issues/193>`_)
+
+
+Bugfixes
+--------
+
+- Pin markupsafe to 2.0.1 to fix incompatibility with jinja2 ^2.10. (PR 184) (`#184 <https://github.com/bio-phys/MDBenchmark/issues/184>`_)
+- Fix bug when plotting cpu-/gpu-data only with 'version3-categories'. (PR 192) (`#192 <https://github.com/bio-phys/MDBenchmark/issues/192>`_)
+- Don't use deprecated kwarg 'type' in matplotlib.pyplot.savefig. (PR 195) (`#195 <https://github.com/bio-phys/MDBenchmark/issues/195>`_)
+
+
 3.0.1 (2020-10-09)
 ==================
 

README.rst

@@ -11,8 +11,8 @@ Benchmark molecular dynamics simulations
 .. image:: https://img.shields.io/pypi/l/mdbenchmark.svg
     :target: https://pypi.python.org/pypi/mdbenchmark
 
-.. image:: https://travis-ci.org/bio-phys/MDBenchmark.svg?branch=develop
-    :target: https://travis-ci.org/bio-phys/MDBenchmark
+.. image:: https://github.com/bio-phys/MDBenchmark/actions/workflows/tests.yml/badge.svg?branch=develop
+    :target: https://github.com/bio-phys/MDBenchmark/actions/workflows/tests.yml
 
 .. image:: https://readthedocs.org/projects/mdbenchmark/badge/?version=latest&style=flat
     :target: https://mdbenchmark.readthedocs.io/en/latest/

docs/conf.py

@@ -61,7 +61,7 @@
 # The short X.Y version.
 version = "3.0"
 # The full version, including alpha/beta/rc tags.
-release = "3.0.1"
+release = "3.0.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/index.rst

@@ -15,8 +15,8 @@ MDBenchmark: Benchmark molecular dynamics simulations
 .. image:: https://img.shields.io/pypi/l/mdbenchmark.svg
     :target: https://pypi.python.org/pypi/mdbenchmark
 
-.. image:: https://travis-ci.org/bio-phys/MDBenchmark.svg?branch=develop
-    :target: https://travis-ci.org/bio-phys/MDBenchmark
+.. image:: https://github.com/bio-phys/MDBenchmark/actions/workflows/tests.yml/badge.svg?branch=develop
+    :target: https://github.com/bio-phys/MDBenchmark/actions/workflows/tests.yml
 
 .. image:: https://codecov.io/gh/bio-phys/MDBenchmark/branch/develop/graph/badge.svg
     :target: https://codecov.io/gh/bio-phys/MDBenchmark

docs/plot.rst

@@ -75,10 +75,10 @@ To change the x-axis label from number of nodes to number of cores you can run::
 
    mdbenchmark plot --plot-cores
 
-Hiding the linear fit
----------------------
+Hiding the optimal scaling
+--------------------------
 
-To create a plot without any linear fit, use the ``--no-fit`` option::
+To create a plot without any optimal scaling graph, use the ``--no-fit`` option::
 
   mdbenchmark plot --no-fit
 
@@ -118,4 +118,4 @@ By default a small watermark will be placed in the top left corner of every plot
 
 You are free to use your plots with and without the watermark, whereever you like, but we kindly ask you to cite our `latest DOI`_ from Zenodo. In this way, more people will notice MDBenchmark and start optimizing their use of high performance computing resources.
 
-.. _latest DOI: https://zenodo.org/record/1156082
+.. _latest DOI: https://zenodo.org/record/1156082

mdbenchmark/__version__.py

@@ -17,4 +17,4 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with MDBenchmark.  If not, see <http://www.gnu.org/licenses/>
-VERSION = "3.0.1"
+VERSION = "3.0.2"

mdbenchmark/cli/commands.py

@@ -292,7 +292,7 @@ def generate(
 )
 @click.option(
     "--fit/--no-fit",
-    help="Fit a line through the first two data points, indicating linear scaling.",
+    help="Fit a line through the first data point, indicating optimal scaling.",
     show_default=True,
     default=True,
 )

mdbenchmark/cli/plot.py

@@ -26,7 +26,6 @@
 from matplotlib.figure import Figure
 
 from mdbenchmark import console
-from mdbenchmark.math import calc_slope_intercept, lin_func
 from mdbenchmark.mdengines import SUPPORTED_ENGINES
 from mdbenchmark.utils import generate_output_name
 from mdbenchmark.versions import VersionFactory
@@ -60,19 +59,11 @@ def get_xsteps(size, min_x, plot_cores, xtick_step):
 
 
 def plot_projection(df, selection, color, performance_column, ax=None):
-    # Grab x and y values
-    xs = df[selection].iloc[0:2].values.tolist()
-    ys = df[performance_column].iloc[0:2].values.tolist()
-
-    # Calculate slope and intercept
-    p1, p2 = list(zip(xs, ys))
-    slope, intercept = calc_slope_intercept(p1, p2)
-
-    # Plot the projection
-    xstep = np.diff(xs)
-    xmax = (df[selection].iloc[-1] + xstep).tolist()
-    xs = np.array([0] + xs + xmax)
-    ax.plot(xs, lin_func(xs, slope, intercept), ls="--", color=color, alpha=0.5)
+    xs = df[selection].values
+    ys = df[performance_column].values
+    xs = np.concatenate((np.array([0]), xs))
+    yp = ys[0] * xs / xs[1]
+    ax.plot(xs, yp, ls="--", color=color, alpha=0.5)
 
     return ax
 
@@ -150,13 +141,15 @@ def plot_over_group(df, plot_cores, fit, performance_column, ax=None):
 
 
 def filter_dataframe_for_plotting(df, host_name, module_name, gpu, cpu):
+    gpu_col = "use_gpu" if "use_gpu" in df.columns else "gpu"
+
     if gpu and cpu:
         console.info("Plotting GPU and CPU data.")
     elif gpu and not cpu:
-        df = df[df.gpu]
+        df = df[df[gpu_col]]
         console.info("Plotting GPU data only.")
     elif cpu and not gpu:
-        df = df[~df.gpu]
+        df = df[~df[gpu_col]]
         console.info("Plotting CPU data only.")
     elif not cpu and not gpu:
         console.error("CPU and GPU not set. Nothing to plot. Exiting.")
@@ -288,10 +281,6 @@ def do_plot(
         output_name = "{}.{}".format(output_name, output_format)
 
     fig.savefig(
-        output_name,
-        type=output_format,
-        bbox_extra_artists=(legend,),
-        bbox_inches="tight",
-        dpi=dpi,
+        output_name, bbox_extra_artists=(legend,), bbox_inches="tight", dpi=dpi,
     )
     console.info("The plot was saved as '{}'.", output_name)