dapper 1.4.0__tar.gz → 1.5.0__tar.gz

{dapper-1.4.0 → dapper-1.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dapper
-Version: 1.4.0
+Version: 1.5.0
 Summary: DAPPER benchmarks the performance of data assimilation (DA) methods.
 Author: Patrick N. Raanes
 Author-email: patrick.n.raanes@gmail.com
@@ -14,13 +14,14 @@ Classifier: Topic :: Scientific/Engineering :: Mathematics
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.7
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 Provides-Extra: Qt
-Provides-Extra: dev
+Provides-Extra: debug
 Provides-Extra: test
 Provides-Extra: lint
 Provides-Extra: build
+Provides-Extra: dev
 License-File: LICENCE.txt
 
 It is usually best to install from source (github),

{dapper-1.4.0 → dapper-1.5.0}/README.md

@@ -91,7 +91,7 @@ Also see its [drawbacks](#similar-projects).
 
 Successfully tested on Linux/Mac/Windows.
 
-### Prerequisite: Python>=3.7 (3.9 on Windows)
+### Prerequisite: Python>=3.9
 
 If you're an expert, setup a python environment however you like.
 Otherwise:
@@ -105,7 +105,7 @@ conda activate dapper-env
 python --version
 ```
 
-Ensure the printed version is 3.7 or more.  
+Ensure the printed version is 3.9 or more.  
 *Keep using the same terminal for the commands below.*
 
 ### Install

{dapper-1.4.0 → dapper-1.5.0}/dapper/__init__.py

@@ -4,7 +4,7 @@
 .. include:: ./README.md
 """
 
-__version__ = "1.4.0"
+__version__ = "1.5.0"
 
 # A parsimonious list of imports used in the examples
 from .dpr_config import rc

{dapper-1.4.0 → dapper-1.5.0}/dapper/tools/liveplotting.py

@@ -21,7 +21,6 @@ argument of the `HMM.liveplotter` and default liveplotters defined in this modul
 is the name of the corresponding liveplotting classes/functions.
 """
 
-import matplotlib as mpl
 import numpy as np
 import scipy.linalg as sla
 from matplotlib import pyplot as plt
@@ -579,17 +578,9 @@ class correlations:
         if Nx <= 1003:
             C = np.eye(Nx)
             # Mask half
-            mask = np.zeros_like(C, dtype=np.bool)
+            mask = np.zeros_like(C, dtype=bool)
             mask[np.tril_indices_from(mask)] = True
-            # Make colormap. Log-transform cmap,
-            # but not internally in matplotlib,
-            # so as to avoid transforming the colorbar too.
             cmap = plt.get_cmap('RdBu_r')
-            trfm = mpl.colors.SymLogNorm(linthresh=0.2, linscale=0.2,
-                                         base=np.e, vmin=-1, vmax=1)
-            cmap = cmap(trfm(np.linspace(-0.6, 0.6, cmap.N)))
-            cmap = mpl.colors.ListedColormap(cmap)
-            #
             VM   = 1.0  # abs(np.percentile(C,[1,99])).max()
             im   = ax.imshow(C, cmap=cmap, vmin=-VM, vmax=VM)
             # Colorbar

{dapper-1.4.0 → dapper-1.5.0}/dapper/tools/series.py

@@ -215,14 +215,15 @@ class FAUSt(DataSeries, StatPrint):
         - `store_u`    : if False: only the current value is stored.
         - `kwargs`     : passed on to ndarrays.
         """
-        self.f     = np.full((Ko+1,)+item_shape, nan, **kwargs)
-        self.a     = np.full((Ko+1,)+item_shape, nan, **kwargs)
+        fill_value = -99 if kwargs.get("dtype", None) is int else nan
+        self.f     = np.full((Ko+1,)+item_shape, fill_value, **kwargs)
+        self.a     = np.full((Ko+1,)+item_shape, fill_value, **kwargs)
         if store_s:
-            self.s = np.full((Ko+1,)+item_shape, nan, **kwargs)
+            self.s = np.full((Ko+1,)+item_shape, fill_value, **kwargs)
         if store_u:
-            self.u = np.full((K   + 1,)+item_shape, nan, **kwargs)
+            self.u = np.full((K   + 1,)+item_shape, fill_value, **kwargs)
         else:
-            self.u = np.full((1,)+item_shape, nan, **kwargs)
+            self.u = np.full((1,)+item_shape, fill_value, **kwargs)
 
     # We could just store the input values for these attrs, but using
     # property => Won't be listed in vars(self), and un-writeable.

{dapper-1.4.0 → dapper-1.5.0}/dapper/tools/viz.py

@@ -463,7 +463,7 @@ def plot_rank_histogram(stats):
 
     has_been_computed = \
         hasattr(stats, 'rh') and \
-        not all(stats.rh.a[-1] == array(np.nan).astype(int))
+        not all(stats.rh.a[-1] == array(-99))
 
     fig, ax = place.freshfig("Rank histogram", figsize=(6, 3))
     ax.set_title('(Mean of marginal) rank histogram (_a)')

{dapper-1.4.0 → dapper-1.5.0}/dapper/xp_process.py

@@ -52,7 +52,8 @@ class SparseSpace(dict):
     The most important method is `nest`,
     which is used (by `xpSpace.table_tree`) to print and plot results.
     This is essentially a "groupby" operation, and indeed the case could
-    be made that this class should be replaced by `pandas.DataFrame`.
+    be made that this class should be replaced by `pandas.DataFrame`,
+    or better yet: <https://github.com/pydata/xarray>.
 
     The `__getitem__` is quite flexible, allowing accessing by:
 

{dapper-1.4.0 → dapper-1.5.0}/dapper.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dapper
-Version: 1.4.0
+Version: 1.5.0
 Summary: DAPPER benchmarks the performance of data assimilation (DA) methods.
 Author: Patrick N. Raanes
 Author-email: patrick.n.raanes@gmail.com
@@ -14,13 +14,14 @@ Classifier: Topic :: Scientific/Engineering :: Mathematics
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.7
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 Provides-Extra: Qt
-Provides-Extra: dev
+Provides-Extra: debug
 Provides-Extra: test
 Provides-Extra: lint
 Provides-Extra: build
+Provides-Extra: dev
 License-File: LICENCE.txt
 
 It is usually best to install from source (github),

{dapper-1.4.0 → dapper-1.5.0}/dapper.egg-info/requires.txt

@@ -1,12 +1,12 @@
-scipy>=1.1
-ipython>=5.1
-jedi<0.18
+scipy>=1.10
 jupyter
-matplotlib~=3.2.2
+ipdb
+ipython>=5.1
+tornado==6.1
+matplotlib~=3.7
 mpl-tools==0.2.50
 tqdm~=4.31
 pyyaml
-ipdb
 colorama~=0.4.1
 tabulate~=0.8.3
 dill==0.3.2
@@ -24,6 +24,11 @@ twine
 pdoc
 jupytext
 
+[debug]
+line_profiler
+pre-commit
+pdbpp>=0.10.3
+
 [dev]
 line_profiler
 pre-commit

{dapper-1.4.0 → dapper-1.5.0}/examples/basic_1.py

@@ -49,6 +49,7 @@ print(xp.avrgs.tabulate(['rmse.a', 'rmv.a']))
 
 # #### Replay liveplotters
 
+# Does not work on Colab
 xp.stats.replay(
     # speed=.6
 )

{dapper-1.4.0 → dapper-1.5.0}/setup.py

@@ -17,16 +17,18 @@ from setuptools import find_packages, setup
 DOCLINES = __doc__.split('\n')
 
 # Dependencies
+# Why pin?: https://github.com/nansencenter/DAPPER/issues/41#issuecomment-1381616971
 INSTALL_REQUIRES = [
-    'scipy>=1.1',
-    'ipython>=5.1',
-    'jedi<0.18',  # ipython/issues/12740
+    'scipy>=1.10',
     'jupyter',
-    'matplotlib~=3.2.2',  # use Colab's version (newer wont work there)
+    'ipdb',
+    'ipython>=5.1',
+    # 'jedi<0.18',  # ipython/issues/12740
+    'tornado==6.1',  # 6.2 breaks Jupyter plots (tested on Mac, Linux)
+    'matplotlib~=3.7',
     'mpl-tools==0.2.50',
     'tqdm~=4.31',
     'pyyaml',
-    'ipdb',
     'colorama~=0.4.1',
     'tabulate~=0.8.3',
     'dill==0.3.2',  # >=0.3.1.1 for dataclass. Pin vers. to equal GCP.
@@ -39,7 +41,7 @@ INSTALL_REQUIRES = [
 
 EXTRAS = {
     'Qt': ['PyQt5', 'qtpy'],
-    'dev': ['line_profiler', 'pre-commit', 'pdbpp>=0.10.3'],
+    'debug': ['line_profiler', 'pre-commit', 'pdbpp>=0.10.3'],
     'test': ['tox', 'coverage>=5.1', 'pytest',
              'pytest-cov', 'pytest-sugar', 'pytest-benchmark',
              'pytest-clarity', 'pytest-xdist', 'pytest-timeout'],
@@ -48,7 +50,7 @@ EXTRAS = {
     # 'flake8-docstrings', 'flake8-bugbear', 'flake8-comprehensions'],
     'build': ['twine', 'pdoc', 'jupytext'],
 }
-EXTRAS['dev'] += EXTRAS['test'] + EXTRAS['lint'] + EXTRAS['build']
+EXTRAS['dev'] = EXTRAS['debug'] + EXTRAS['test'] + EXTRAS['lint'] + EXTRAS['build']
 
 
 def find_version(*file_paths):
@@ -90,7 +92,7 @@ setup(
     # >=3.7 for dataclass, capture_output, dict ordering, np>=1.20.
     # ==3.7 for Colab
     # ==3.9 for the DAPPER/GCP cluster, since dill isn't compat. across versions.
-    python_requires='>=3.7',
+    python_requires='>=3.9',
     install_requires=INSTALL_REQUIRES,
     extras_require=EXTRAS,