Change minimum versions and remove compatibility fixes (soft-matter#656)

* Test against numba 0.45 on Py37

* Increase minimum versions

* Bump travis (doc build)

* Bump doc build env

.github/workflows/test-pip.yml

@@ -10,23 +10,14 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          # "Legacy" environments: oldest supported versions, without and with optional dependencies
-          - python: 3.5
-            display_name: "no optional deps"
-            numpy: "numpy==1.13.*"
-            deps: "scipy==0.19.* matplotlib==2.0.* pandas==0.20.* pyyaml"
-          - python: 3.5
-            display_name: "no numba"
-            numpy: "numpy==1.13.*"
-            deps: "scipy==0.19.* matplotlib==2.0.* pillow==4.2.* pandas==0.20.* scikit-image==0.13.* tables==3.3.* scikit-learn==0.19.* pyyaml==3.12"
           # 2017
           - python: 3.6
             numpy: "numpy==1.14.*"
             deps: "scipy==1.1.* matplotlib==2.1.* pillow==4.3.* pandas==0.22.* scikit-image==0.13.* tables==3.4.* scikit-learn==0.19.* pyyaml==3.12 numba==0.32.* llvmlite==0.17.*"
           # 2018
           - python: 3.7
             numpy: "numpy==1.16.*"
-            deps: "scipy==1.3.* matplotlib==2.2.* pillow==5.3.* pandas==0.23.* scikit-image==0.14.* tables==3.5.* scikit-learn==0.20.* pyyaml==3.13 numba==0.39.* llvmlite==0.24."
+            deps: "scipy==1.3.* matplotlib==2.2.* pillow==5.3.* pandas==0.23.* scikit-image==0.14.* tables==3.5.* scikit-learn==0.20.* pyyaml==3.13 numba==0.45.* llvmlite==0.29.*"
           # 2019
           - python: 3.8
             numpy: "numpy==1.18.*"

.travis.yml

@@ -2,9 +2,9 @@ language: python
 
 jobs:
   include:
-    # Python 3, circa September 2017 (Anaconda 5.0.0), used for building docs
-    - python: "3.5"
-      env: DEPS="numpy=1.13.1 scipy=0.19.1 matplotlib=2.0.2 pillow=4.2.1 pandas=0.20.3 scikit-image=0.13.0 pytables numba=0.35.0 scikit-learn=0.19.0 pyyaml" BUILD_DOCS=true
+    # Note: Apr 2, 2021. This is only used for building the docs now, testing happens in Github actions.
+    - python: "3.8"
+      env: DEPS="numpy scipy matplotlib pillow pandas scikit-image pytables numba scikit-learn pyyaml" BUILD_DOCS=true
 
 install:
   - conda update --yes conda
@@ -28,7 +28,7 @@ script:
   - |
     if [ $BUILD_DOCS == true ]; then
       conda config --append channels conda-forge
-      conda install --yes ipython=5.1.0 sphinx=1.4.8 numpydoc=0.6.0 nbconvert=4.2.0 sphinx_bootstrap_theme=0.4
+      conda install --yes ipython sphinx numpydoc nbconvert sphinx_bootstrap_theme
       cd $TRAVIS_BUILD_DIR/..
       git clone https://github.com/soft-matter/trackpy-examples.git
       cd trackpy/doc

setup.py

@@ -32,16 +32,14 @@
     author = "Trackpy Contributors",
     author_email = "[email protected]",
     url = "https://github.com/soft-matter/trackpy",
-    install_requires = ['numpy>=1.9', 'scipy>=0.14',
-                        'pandas>=0.15', 'pyyaml', 'matplotlib'],
-    python_requires=">=3.5",
+    install_requires = ['numpy>=1.14', 'scipy>=1.1', 'pandas>=0.22', 'pyyaml', 'matplotlib'],
+    python_requires=">=3.6",
     classifiers=[
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.5",
         "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3 :: Only",
+        "Programming Language :: Python :: 3.9",
     ],
     packages = ['trackpy', 'trackpy.refine', 'trackpy.linking', 'trackpy.locate_functions'],
     long_description = descr,

trackpy/linking/legacy.py

@@ -5,9 +5,10 @@
 
 import numpy as np
 import pandas as pd
+from scipy.spatial import cKDTree
 
 from ..try_numba import NUMBA_AVAILABLE
-from ..utils import pandas_sort, cKDTree, validate_tuple, is_isotropic
+from ..utils import pandas_sort, validate_tuple, is_isotropic
 from .utils import (TrackUnstored, points_to_arr, UnknownLinkingError,
                     SubnetOversizeException)
 from .subnetlinker import (recursive_linker_obj, nonrecursive_link, drop_link,

trackpy/linking/subnet.py

@@ -3,9 +3,10 @@
 
 import numpy as np
 import pandas as pd
+from scipy.spatial import cKDTree
 
 from .utils import points_to_arr
-from ..utils import default_pos_columns, cKDTree
+from ..utils import default_pos_columns
 
 try:
     from sklearn.neighbors import BallTree

trackpy/motion.py

@@ -4,8 +4,7 @@
 
 import warnings
 from warnings import warn
-from .utils import (pandas_sort, pandas_concat, pandas_rolling,
-                    guess_pos_columns)
+from .utils import pandas_sort, pandas_concat, guess_pos_columns
 
 
 def msd(traj, mpp, fps, max_lagtime=100, detail=False, pos_columns=None):
@@ -287,7 +286,7 @@ def compute_drift(traj, smoothing=0, pos_columns=None):
     mask = (f_diff['particle'] == 0) & (f_diff['frame_diff'] == 1)
     dx = f_diff.loc[mask, list(pos_columns) + ['frame']].groupby('frame').mean()
     if smoothing > 0:
-        dx = pandas_rolling(dx, smoothing, min_periods=0)
+        dx = dx.rolling(smoothing, min_periods=0).mean()
     return dx.cumsum()
 
 

trackpy/static.py

@@ -1,4 +1,5 @@
-from .utils import cKDTree, guess_pos_columns
+from scipy.spatial import cKDTree
+from .utils import guess_pos_columns
 import numpy as np
 from pandas import DataFrame
 

trackpy/tests/common.py

@@ -3,7 +3,8 @@
 import numpy as np
 from numpy.testing import assert_allclose, assert_equal, assert_array_equal
 import trackpy as tp
-from trackpy.utils import cKDTree, pandas_sort, make_pandas_strict
+from scipy.spatial import cKDTree
+from trackpy.utils import pandas_sort, make_pandas_strict
 from trackpy.artificial import SimulatedImage
 from matplotlib.pyplot import imread
 

trackpy/tests/test_legacy_linking.py

@@ -12,8 +12,7 @@
 from trackpy.linking.legacy import (link, link_df, link_df_iter,
                                     PointND, Hash_table, strip_diagnostics,
                                     SubnetOversizeException)
-from trackpy.utils import (is_pandas_since_016,
-                           pandas_sort, pandas_concat, validate_tuple)
+from trackpy.utils import pandas_sort, pandas_concat, validate_tuple
 from trackpy.tests.common import StrictTestCase, assert_traj_equal
 
 

trackpy/tests/test_reproducibility.py

@@ -2,26 +2,17 @@
 import numpy as np
 import pandas as pd
 from numpy.testing import assert_array_equal, assert_allclose
+from scipy.spatial import cKDTree
 
 import trackpy as tp
 from trackpy.preprocessing import invert_image
-from trackpy.utils import cKDTree, pandas_iloc, is_scipy_since_100
 from trackpy.tests.common import TrackpyImageSequence
 from trackpy.tests.common import assert_traj_equal, StrictTestCase
 
 path, _ = os.path.split(os.path.abspath(__file__))
 
 
-# The reproducibility tests differ depending on the Scipy version, because of
-# changed rounding properties of `scipy.ndimage.filters.uniform_filter1d`. These
-# changes propagate via trackpy's preprocessing into the tested values in the
-# following tests: `test_find_bp`, `test_locate`, `test_refine`, and
-# `test_characterize`. See GH issue #459.
-if is_scipy_since_100:
-    reproduce_fn = 'reproducibility_v0.4.npz'
-else:
-    reproduce_fn = 'reproducibility_v0.4_pre_scipy_v1.0.npz'
-reproduce_fn = os.path.join(path, 'data', reproduce_fn)
+reproduce_fn = os.path.join(path, 'data', 'reproducibility_v0.4.npz')
 
 
 def compare_pos_df(actual, expected, pos_atol=0.001, lost_atol=1):
@@ -53,12 +44,12 @@ def compare_pos_df(actual, expected, pos_atol=0.001, lost_atol=1):
         i_appeared1 = np.argwhere(~np.in1d(np.arange(len(coords1)),
                                            np.concatenate(
                                                [i_equal0, i_dev0]))).ravel()
-        lost0.append(pandas_iloc(expected_frame, i_lost0).index.values)
-        appeared1.append(pandas_iloc(actual_frame, i_appeared1).index.values)
-        dev0.append(pandas_iloc(expected_frame, i_dev0).index.values)
-        dev1.append(pandas_iloc(actual_frame, i_dev1).index.values)
-        equal0.append(pandas_iloc(expected_frame, i_equal0).index.values)
-        equal1.append(pandas_iloc(actual_frame, i_equal1).index.values)
+        lost0.append(expected_frame.iloc[i_lost0].index.values)
+        appeared1.append(actual_frame.iloc[i_appeared1].index.values)
+        dev0.append(expected_frame.iloc[i_dev0].index.values)
+        dev1.append(actual_frame.iloc[i_dev1].index.values)
+        equal0.append(expected_frame.iloc[i_equal0].index.values)
+        equal1.append(actual_frame.iloc[i_equal1].index.values)
 
     return np.concatenate(lost0), np.concatenate(appeared1), \
            (np.concatenate(dev0), np.concatenate(dev1)), \

trackpy/utils.py

@@ -17,51 +17,13 @@
 
 import trackpy
 
-# Set is_pandas_since_016 for use elsewhere.
-# Pandas >= 0.16.0 lets us check if a DataFrame is a view.
-try:
-    is_pandas_since_016 = (LooseVersion(pd.__version__) >=
-                           LooseVersion('0.16.0'))
-except ValueError:  # Probably a development version
-    is_pandas_since_016 = True
 
-try:
-    is_pandas_since_017 = (LooseVersion(pd.__version__) >=
-                           LooseVersion('0.17.0'))
-except ValueError:  # Probably a development version
-    is_pandas_since_017 = True
-
-try:
-    is_pandas_since_018 = (LooseVersion(pd.__version__) >=
-                           LooseVersion('0.18.0'))
-except ValueError:  # Probably a development version
-    is_pandas_since_018 = True
 try:
     is_pandas_since_023 = (LooseVersion(pd.__version__) >=
                            LooseVersion('0.23.0'))
 except ValueError:  # Probably a development version
     is_pandas_since_023 = True
 
-# Wrap the scipy cKDTree to work around a bug in scipy 0.18.0
-try:
-    is_scipy_018 = LooseVersion(scipy.__version__) == LooseVersion('0.18.0')
-except ValueError:  # Probably a development version
-    is_scipy_018 = False
-
-
-if is_scipy_018:
-    from scipy.spatial import KDTree as cKDTree
-    warnings.warn("Due to a bug in Scipy 0.18.0, the (faster) cKDTree cannot "
-                  "be used. For better linking performance, upgrade or "
-                  "downgrade scipy.")
-else:
-    from scipy.spatial import cKDTree
-
-try:
-    is_scipy_since_100 = LooseVersion(scipy.__version__) >= LooseVersion('1.0.0')
-except ValueError:  # Probably a development version
-    is_scipy_since_100 = True
-
 # Emit warnings in refine.least_squares for scipy 1.5
 try:
     is_scipy_15 = LooseVersion("1.5.0") <= LooseVersion(scipy.__version__) < LooseVersion('1.6.0')
@@ -312,11 +274,8 @@ def quiet(suppress=True):
     else:
         trackpy.logger.setLevel(logging.INFO)
 
-def _pandas_sort_pre_017(df, by, *args, **kwargs):
-    """Use sort() to sort a DataFrame"""
-    return df.sort(*args, columns=by, **kwargs)
 
-def _pandas_sort_post_017(df, by, *args, **kwargs):
+def pandas_sort(df, by, *args, **kwargs):
     """
     Use sort_values() to sort a DataFrame
     This raises a ValueError if the given value is both
@@ -330,39 +289,6 @@ def _pandas_sort_post_017(df, by, *args, **kwargs):
         df.index.name += '_index'
     return df.sort_values(*args, by=by, **kwargs)
 
-if is_pandas_since_017:
-    pandas_sort = _pandas_sort_post_017
-else:
-    pandas_sort = _pandas_sort_pre_017
-
-def _pandas_iloc_pre_016(df, inds):
-    """Workaround for bug, iloc with empty list, in pandas < 0.16"""
-    if len(inds) > 0:
-        return df.iloc[inds]
-    else:
-        return df.iloc[:0]
-
-def _pandas_iloc_since_016(df, inds):
-    return df.iloc[inds]
-
-if is_pandas_since_016:
-    pandas_iloc = _pandas_iloc_since_016
-else:
-    pandas_iloc = _pandas_iloc_pre_016
-
-def _pandas_rolling_pre_018(df, window, *args, **kwargs):
-    """Use rolling_mean() to compute a rolling average"""
-    return pd.rolling_mean(df, window, *args, **kwargs)
-
-def _pandas_rolling_since_018(df, window, *args, **kwargs):
-    """Use rolling() to compute a rolling average"""
-    return df.rolling(window, *args, **kwargs).mean()
-
-if is_pandas_since_018:
-    pandas_rolling = _pandas_rolling_since_018
-else:
-    pandas_rolling = _pandas_rolling_pre_018
-
 
 def _pandas_concat_post_023(*args, **kwargs):
     """Pass sort = False. Breaks API by not sorting, but we don't care. """