Merge pull request #31 from SimoneMartino98/minor_fixes

Merging this pull request, which solves a few minor issues: * #8 added dev installation to the README * #14 updated onion documentation * #30 added onion-clustering to dependencies and removed it from the dev dependancies ones * Updated the maintainers to include @matteobecchi and @SimoneMartino98 Thank you, @SimoneMartino98
GMPavanLab · Sep 10, 2024 · 6e4d1ba · 6e4d1ba
2 parents 7056001 + e5f58ff
commit 6e4d1ba
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diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
@@ -15,7 +15,7 @@ jobs:
           python-version: "3.10"
           cache: "pip"
       - run: pip install -e '.[dev]'
-      - run: ruff .
+      - run: ruff check .
   mypy:
     runs-on: ubuntu-22.04
     steps:

diff --git a/README.rst b/README.rst
@@ -1,5 +1,7 @@
 :maintainers:
-    `andrewtarzia <https://github.com/andrewtarzia/>`_
+    `andrewtarzia <https://github.com/andrewtarzia/>`_;
+    `matteobecchi <https://github.com/matteobecchi/>`_;
+    `simonemartino <https://github.com/SimoneMartino98/>`_
 :documentation: https://dynsight.readthedocs.io
 
 Installation
@@ -10,6 +12,20 @@ To get ``dynsight``, you can install it with pip::
     $ pip install dynsight
 
 
+Developer Setup
+===============
+
+1. Install `just`_.
+2. In a new virtual environment run using Python 3.10::
+
+    $ just dev
+
+3. Run code checks::
+    
+    $ just check
+
+.. _`just`: https://github.com/casey/just
+
 Examples
 ========
 

diff --git a/docs/source/onion.rst b/docs/source/onion.rst
@@ -103,6 +103,6 @@ Example: clustering of multivariate time-series
 
   OnionMulti <_autosummary/dynsight.onion.OnionMulti.rst>
 
-The code for performing clustering on multi time-series can be found in ``examples/onion_multi.py``. The only difference in the usage is that when you run the script you have to specify all the input files, each one containing a different variable:
+The code for performing clustering on multi time-series can be found in ``examples/onion_multi.py``. The only differences is that the input file has to be an .npy or .npz containing a numpy.ndarray with shape (D, N, T), where D is the number of variables (2 or 3). It is then called with
 
-``python3 onion_multi.py path/to/input/file_0.npy path/to/input/file_1.npy``
+``python3 onion_multi.py path/to/input/file.npy``
diff --git a/examples/file_handling.py b/examples/file_handling.py
@@ -2,10 +2,11 @@
 import pathlib
 import sys
 
-import dynsight
 import h5py
 from MDAnalysis import Universe
 
+import dynsight
+
 logging.basicConfig(
     level=logging.INFO,
     format="%(asctime)s | %(levelname)s | %(message)s",

diff --git a/examples/lens.py b/examples/lens.py
@@ -2,10 +2,11 @@
 import pathlib
 import sys
 
-import dynsight
 import h5py
 import matplotlib.pyplot as plt
 
+import dynsight
+
 logging.basicConfig(
     level=logging.INFO,
     format="%(asctime)s | %(levelname)s | %(message)s",

diff --git a/examples/time_soap.py b/examples/time_soap.py
@@ -4,11 +4,12 @@
 import pathlib
 import sys
 
-import dynsight
 import h5py
 import matplotlib.pyplot as plt
 import numpy as np
 
+import dynsight
+
 logging.basicConfig(
     level=logging.INFO,
     format="%(asctime)s | %(levelname)s | %(message)s",

diff --git a/pyproject.toml b/pyproject.toml
@@ -6,11 +6,14 @@ build-backend = "setuptools.build_meta"
 name = "dynsight"
 maintainers = [
   { name = "Andrew Tarzia", email = "andrew.tarzia@gmail.com" },
+  { name = "Matteo Becchi", email = "bechmath@gmail.com"},
+  { name = "Simone Martino", email = "s.martino0898@gmail.com"},
 ]
 
 dependencies = [
   "cpctools",
   "dscribe >1.2.0, <=1.2.2",
+  "onion-clustering",
 ]
 # Set by cpctools.
 requires-python = "<3.11,>=3.8"
@@ -30,7 +33,6 @@ dev = [
   "twine",
   "furo",
   "numba",
-  "onion-clustering",
 ]
 
 [project.urls]

diff --git a/tests/lens/conftest.py b/tests/lens/conftest.py
@@ -2,11 +2,12 @@
 
 import pathlib  # noqa: TCH003
 
-import dynsight
 import MDAnalysis
 import numpy as np
 import pytest
 
+import dynsight
+
 
 def fewframeuniverse(
     trajectory: list[list[list[int]]],

diff --git a/tests/lens/test_count_neigh.py b/tests/lens/test_count_neigh.py
@@ -2,11 +2,12 @@
 
 from typing import TYPE_CHECKING
 
-import dynsight
 import MDAnalysis
 import numpy as np
 from numpy.testing import assert_array_equal
 
+import dynsight
+
 from .utilities import is_sorted
 
 if TYPE_CHECKING:

diff --git a/tests/lens/test_emulate_lens.py b/tests/lens/test_emulate_lens.py
@@ -2,10 +2,11 @@
 
 from typing import TYPE_CHECKING
 
-import dynsight
 import numpy as np
 from numpy.testing import assert_array_almost_equal
 
+import dynsight
+
 if TYPE_CHECKING:
     import pathlib
 

diff --git a/tests/lens/test_lens.py b/tests/lens/test_lens.py
@@ -1,9 +1,10 @@
 from pathlib import Path
 
-import dynsight
 import h5py
 import numpy as np
 
+import dynsight
+
 
 def test_lens_signals() -> None:
     """Test the consistency of LENS calculations with a control calculation.

diff --git a/tests/lens/test_special_lens.py b/tests/lens/test_special_lens.py
@@ -1,8 +1,9 @@
-import dynsight
 import MDAnalysis
 import numpy as np
 from numpy.testing import assert_array_equal
 
+import dynsight
+
 
 def test_special_lens(lensfixtures: MDAnalysis.Universe) -> None:
     """Test :class:`.` SOMETHING.

diff --git a/tests/onion/output_multi/final_states.txt b/tests/onion/output_multi/final_states.txt
@@ -1,9 +1,4 @@
 #center_coords, semiaxis, fraction_of_data
-[-9.217402795162704, 0.8671904740262623] [33.945254636130386, 22.46005166079635] 0.73
-[17.654521861274752, 40.70380484547634] [10.189158728161274, 22.988963620172285] 0.074
-[-0.9549435822358326, 21.694181975980854] [42.81775243259092, 10.799453604676156] 0.066
-[8.762548476254363, -25.782312046886265] [18.606829594259793, 13.502135433544812] 0.062
-[20.888067778317723, 2.4339018657723788] [9.204690309963093, 17.1340229561863] 0.02
-[47.46513497795252, -39.11984327088997] [89.66256446734177, 10.351158875005384] 0.01
-[40.5609722076551, -1.4023316935773076] [6.597585788934516, 17.391048803811703] 0.008
-[-20.557255476627713, 27.57182121053266] [6.737239162308862, 10.523198493586497] 0.004
+[-4.884215210771138, 5.875825445555712] [42.49235200752218, 39.105473589727524] 0.992
+[16.889434998848554, 42.960777466708876] [23.023489207065, 35.921315853945174] 0.006
+[-42.34473154834106, 25.025975116712356] [5.261471202436318, 3.7104547182238203] 0.002
diff --git a/tests/onion/output_multi/fraction_0.txt b/tests/onion/output_multi/fraction_0.txt
@@ -1,2 +1,2 @@
 # tau_window	 fraction in ENV0 for different t_smooth
-1.000000000000000000e+01 2.600000000000002309e-02
+1.000000000000000000e+01 0.000000000000000000e+00
diff --git a/tests/onion/output_multi/number_of_states.txt b/tests/onion/output_multi/number_of_states.txt
@@ -1,2 +1,2 @@
 # tau_window	 number_of_states for different t_smooth
-10	9
+10	3
diff --git a/tests/onion/output_uni/final_states.txt b/tests/onion/output_uni/final_states.txt
@@ -1,5 +1,12 @@
+####################################
 # Mu 	 Sigma 	 A 	 state_fraction
--4.438261940387309 13.803915411767766 4164.151761014315 0.824
-32.16777927755445 3.102021970732714 140.28469675425177 0.028
-41.3743936963291 3.834727957507484 203.02063626379885 0.044
-50.941700398008386 3.7730568339013524 425.21039717312294 0.092
+-2.308030920563922 14.897682643328688 4178.444728092517 0.83
+33.702615222102075 4.616618331212346 191.09032200086418 0.036
+42.128752424262075 4.592969491670723 68.4171470337773 0.026
+51.7995729641774 5.435395431244352 490.5824660778189 0.108
+####################################
+# Mu 	 Sigma 	 A 	 state_fraction
+-2.308030920563922 14.897682643328688 4178.444728092517 0.83
+33.702615222102075 4.616618331212346 191.09032200086418 0.036
+42.128752424262075 4.592969491670723 68.4171470337773 0.026
+51.7995729641774 5.435395431244352 490.5824660778189 0.108
diff --git a/tests/onion/output_uni/fraction_0.txt b/tests/onion/output_uni/fraction_0.txt
@@ -1,2 +1,2 @@
 # tau_window	 fraction in ENV0 for different t_smooth
-1.000000000000000000e+01 1.200000000000001066e-02
+1.000000000000000000e+01 0.000000000000000000e+00
diff --git a/tests/onion/output_uni/number_of_states.txt b/tests/onion/output_uni/number_of_states.txt
@@ -1,2 +1,2 @@
 # tau_window	 number_of_states for different t_smooth
-10	5
+10	4
diff --git a/tests/onion/test_multi.py b/tests/onion/test_multi.py
@@ -5,12 +5,13 @@
 from pathlib import Path
 from typing import Generator
 
-import dynsight
 import numpy as np
 import pytest
 
+import dynsight
+
 
-@pytest.fixture()
+@pytest.fixture
 def original_wd() -> Generator[Path, None, None]:
     original_dir = Path.cwd()
 

diff --git a/tests/onion/test_uni.py b/tests/onion/test_uni.py
@@ -5,12 +5,13 @@
 from pathlib import Path
 from typing import Generator
 
-import dynsight
 import numpy as np
 import pytest
 
+import dynsight
+
 
-@pytest.fixture()
+@pytest.fixture
 def original_wd() -> Generator[Path, None, None]:
     original_dir = Path.cwd()
 

diff --git a/tests/soap/test_soap.py b/tests/soap/test_soap.py
@@ -1,9 +1,10 @@
 from pathlib import Path
 
-import dynsight
 import h5py
 import numpy as np
 
+import dynsight
+
 
 def test_soap_vectors() -> None:
     """Test the consistency of SOAP calculations with a control calculation.

diff --git a/tests/soap/test_tsoap.py b/tests/soap/test_tsoap.py
@@ -1,9 +1,10 @@
 from pathlib import Path
 
-import dynsight
 import h5py
 import numpy as np
 
+import dynsight
+
 
 def test_time_soap_vectors() -> None:
     """Test the consistency of tSOAP calculations with a control calculation.