Merge pull request #9 from amritagos/develop

Develop: upgrade ASE etc

.github/workflows/ci.yml

@@ -28,11 +28,16 @@ jobs:
         post-cleanup: 'all'
 
     - if: runner.os == 'Linux'
-      name: Setup xvfb (Linux)
-      run: |
-        sudo apt-get install -y xvfb libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 libxcb-shape0 libglib2.0-0 libgl1-mesa-dev
-        sudo apt-get install '^libxcb.*-dev' libx11-xcb-dev libglu1-mesa-dev libxrender-dev libxi-dev libxkbcommon-dev libxkbcommon-x11-dev
-        sudo /usr/bin/Xvfb $DISPLAY -screen 0 1280x1024x24 &
+        name: Setup xvfb (Linux)
+        run: |
+          sudo apt-get update --fix-missing
+          sudo apt-get install -y xvfb libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 \
+                                  libxcb-render-util0 libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 libxcb-shape0 \
+                                  libglib2.0-0 libgl1-mesa-dev || sudo apt-get install -y libgl1-mesa-glx
+          sudo apt-get install -y '^libxcb.*-dev' libx11-xcb-dev libglu1-mesa-dev libxrender-dev libxi-dev libxkbcommon-dev \
+                                  libxkbcommon-x11-dev
+          export DISPLAY=:99
+          Xvfb :99 -screen 0 1280x1024x24 &
 
     - name: Install the package
       shell: micromamba-shell {0}

README.md

@@ -4,7 +4,7 @@
 
 ## About
 
-Various ways to analyze and visualize solvation shell structures, which wraps [`PyVista`](https://docs.pyvista.org/version/stable/). Meant primarily for analyzing the outputs produced by LAMMPS here. 
+Various ways to analyze and visualize solvation shell structures, which wraps [`PyVista`](https://docs.pyvista.org/version/stable/). Meant primarily for analyzing the outputs produced by LAMMPS, but anything that [ASE](https://gitlab.com/ase/ase) can handle should work.
 
 ## Installation 
 
@@ -48,7 +48,7 @@ In order to debug tests using `pdb`, you can write the command `breakpoint()` in
 
 To see more verbose output from `pytest`, including tests that pass, you can run `pytest -rA`.
 
-Note that `test_hydrogen_bond.py` and `test_plot_octahedral_shell.py` actually compare the results of images created for a single hydrogen bond and for an octahedral shell showing hydrogen bonds formed by the acceptor seventh molecule, respectively. The images compared against are present in the top-level `image_cache_dir` directory.
+Note that `test_hydrogen_bond.py` and `test_plot_octahedral_shell.py` actually compare the results of images created for a single hydrogen bond and for an octahedral shell showing hydrogen bonds formed by the acceptor seventh molecule, respectively. The images compared against are present in the top-level `image_cache_dir` directory. The package [`pytest-pyvista`](https://github.com/pyvista/pytest-pyvista) is used for image verification.
 
 To view a coverage report, run the following from the top-level directory: 
 

environment.yml

@@ -11,32 +11,32 @@ channels:
 #     - {{ compiler('c++') }}
 dependencies:
   - python>=3.10
-  - build<0.10.0
+  - python-build
   - ase>=3.22.1
   - numpy>=1.26.4 # 1.22.4
   - scipy>=1.7.3
   - ipython>=8.26.0
   - pandas>=2.2.2
-  - pyvista==0.43.0
+  - pyvista>=0.43.0
   - pytest-pyvista
   # Dependencies for pyvista
-  - vtk==9.2.6
-  - pillow==10.0.1
-  - imageio==2.31.5
-  - pooch==1.8.0
-  - scooby==0.9.2
+  - vtk>=9.2.6
+  - pillow>=10.0.1
+  - imageio>=2.31.5
+  - pooch>=1.8.0
+  - scooby>=0.9.2
   # Packaging
   - twine
-  - flit==3.9.0
-  - pytest==6.2.5
-  - coverage==6.1.1
-  - pytest-cov==3.0.0
-  - flake8==3.9.2
-  - mypy==0.910
-  - black==22.3.0
-  - isort==5.9.3
-  - autoflake==1.4
-  - flake8-docstrings==1.6.0 
+  - flit>=3.9.0
+  - pytest>=6.2.5
+  - coverage>=6.1.1
+  - pytest-cov>=3.0.0
+  - flake8>=3.9.2
+  - mypy>=0.910
+  - black>=22.3.0
+  - isort>=5.9.3
+  - autoflake>=1.4
+  - flake8-docstrings>=1.6.0 
   - meson-python>=0.16.0
   - pytest-cov>=3.0.0
   # - pip:

pyproject.toml

@@ -5,39 +5,39 @@ build-backend = "mesonpy"
 
 [project]
 name = "solvis-tools"
-version = "0.1.4"
+version = "0.1.5"
 description = "A module for analyzing and visualizing solvation shells in LAMMPS output files, but would work with most files that can be handled by ASE."
 authors = [
     {name = "Amrita Goswami", email = "[email protected]"},
 ]
 classifiers=[
         'Programming Language :: Python :: 3.10']
 dependencies = [
-    "ase == 3.22.1",
+    "ase >= 3.22.1",
     "numpy",
     "scipy >= 1.7.3",
-    "pyvista == 0.43.0",
-    "pillow == 10.0.1",
-    "imageio == 2.31.5",
-    "pooch==1.8.0",
-    "scooby==0.9.2"]
+    "pyvista >= 0.43.0",
+    "pillow >= 10.0.1",
+    "imageio >= 2.31.5",
+    "pooch>=1.8.0",
+    "scooby>=0.9.2"]
 requires-python = ">=3.10"
 readme = "README.md"
 license = {text = "MIT"}
 
 [project.optional-dependencies]
 test = [
-    "pytest==6.2.5",
-    "coverage==6.1.1",
-    "pytest-cov==3.0.0",
+    "pytest>=6.2.5",
+    "coverage>=6.1.1",
+    "pytest-cov>=3.0.0",
 ]
 dev = [
-    "flake8==3.9.2",
-    "mypy==0.910",
-    "black==22.3.0",
-    "isort==5.9.3",
-    "autoflake==1.4",
-    "flake8-docstrings==1.6.0",
+    "flake8>=3.9.2",
+    "mypy>=0.910",
+    "black>=22.3.0",
+    "isort>=5.9.3",
+    "autoflake>=1.4",
+    "flake8-docstrings>=1.6.0",
 ]
 examples = [
     "pandas"

resources/system_oct_hbonds.lammpstrj

@@ -0,0 +1,31 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+22
+ITEM: BOX BOUNDS pp pp pp
+0.0 49.3343262653
+0.0 49.3343262653
+0.0 49.3343262653
+ITEM: ATOMS id type mol x y z
+8342 1 2952 36.7343285501 15.8050824282 11.0866297913
+8343 2 2952 36.4231130904 15.6435884192 11.9790976036
+8344 2 2952 36.0541073213 15.430605905 10.523983995
+51 3 51 38.4269627491 16.7640096871 10.5166861564
+6917 1 2477 37.3705723999 18.4064471724 9.9960275912
+10241 1 3585 38.190079692 16.032697681 8.6381675257
+10242 2 3585 37.7089454164 16.4231842844 7.9063654411
+10243 2 3585 38.5194086342 15.2011958161 8.2921883998
+11081 1 3865 39.5037304337 15.1105580206 10.9930383184
+11082 2 3865 40.4563419719 15.002068572 10.9764231595
+11083 2 3865 39.172385178 14.271094096 11.3171288078
+11231 1 3915 40.1398526826 17.685469079 9.9427187829
+11232 2 3915 40.6050552836 18.3827417874 10.4084777851
+11233 2 3915 40.6345096646 17.568816026 9.1295717459
+6919 2 2477 36.7264230983 18.7590344697 10.6137857894
+6918 2 2477 37.4060896033 19.0546184324 9.2904820606
+4745 1 1753 38.6612581135 17.4564295043 12.4015089326
+4746 2 1753 37.9776645136 18.0020671862 12.7962175922
+4747 2 1753 39.308292735 17.3402502873 13.0994298131
+3417 2 1310 35.3461723311 18.5020561601 12.7963785306
+3416 1 1310 36.205330391 18.8010521733 12.4957046084
+3418 2 1310 36.2695761464 19.7031328123 12.8124575692

tests/test_hydrogen_bonds.py

@@ -32,7 +32,7 @@ def test_single_hbond(verify_image_cache):
         infilename, format="lammps-dump-text"
     )  # Read in the last frame of the trajectory
     # Box size lengths
-    box_len = currentframe.get_cell_lengths_and_angles()[:3]
+    box_len = currentframe.cell.cellpar()[:3]
 
     # Create a SolvationShell object from the solvent
     solvation_shell = solvis.solvation_shell.create_solvation_shell_from_solvent(

tests/test_plot_octahedral_shell.py

@@ -13,7 +13,7 @@ def test_octahedral_shell(verify_image_cache):
     """
     # Input filename
     test_dir = Path(__file__).resolve().parent
-    infilename = test_dir / "../resources/system_oct_hbonds.data"
+    infilename = test_dir / "../resources/system_oct_hbonds.lammpstrj"
     # In the LAMMPS trajectory file, the types of atoms are 1, 2 and 3 for O, H and Fe respectively.
     fe_type = 3
     h_type = 2
@@ -30,10 +30,10 @@ def test_octahedral_shell(verify_image_cache):
 
     # Read in the current frame
     currentframe = read(
-        infilename, format="lammps-data"
+        infilename, format="lammps-dump-text"
     )  # Read in the last frame of the trajectory
     # Box size lengths
-    box_len = currentframe.get_cell_lengths_and_angles()[:3]
+    box_len = currentframe.cell.cellpar()[:3]
 
     # Make a System object
     full_system = solvis.system.System(currentframe, expand_box=True)
@@ -127,7 +127,7 @@ def test_octahedral_shell(verify_image_cache):
                 ["center", iatom_tag],
                 bond_type=1,
                 colorby="bondtype",
-                **bond1_render_opt
+                **bond1_render_opt,
             )
 
     # Change the color of the bond from the seventh atom