updating cross spectral branch (#572)

* pin all python versions to 3.11.0 (#567) * pin all python versions to 3.11.0 * Update .travis.yml * Update rtd_env.yml * Update environment.yml * Update environment.yml * Update testmaster.yml * pin to 3.11.0 * Update .readthedocs.yaml (#568) * Mcpca doc (#570) * ensemblegeoseries docstring fix * ensmultivardecomp doc string fix * mgs docstrings * ms docstrings * mvd docstrings * doc fixes * tick version (#571) * tick version * add requests to setup.py * verbose doc fix --------- Co-authored-by: Alexander James <[email protected]> --------- Co-authored-by: Jordan Landers <[email protected]> Co-authored-by: Julien Emile-Geay <[email protected]>
LinkedEarth · Jun 4, 2024 · deb4b1c · deb4b1c
1 parent 35c3a4c
commit deb4b1c
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diff --git a/.github/workflows/testmaster.yml b/.github/workflows/testmaster.yml
@@ -24,7 +24,7 @@ jobs:
       with:
         activate-environment: pyleo
         environment-file: environment.yml
-        python-version: "3.10"
+        python-version: "3.11.0"
         auto-activate-base: false
 
     - name: Conda list

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -19,7 +19,7 @@ conda:
   environment: doc_build/rtd_env.yml
 
 sphinx:
-  fail_on_warning: true
+  fail_on_warning: false
 
 formats: []
 

diff --git a/.travis.yml b/.travis.yml
@@ -1,6 +1,6 @@
 language: python
 python:
-  - '3.9'
+  - '3.11'
 
 
 before_install:
@@ -15,7 +15,7 @@ before_install:
   - conda info -a
 
 install:
-  - conda create -n pyleoenv python=3.9
+  - conda create -n pyleoenv python=3.11
   - source activate pyleoenv
   - conda install numpy
   - conda install -c conda-forge cartopy

diff --git a/CITATION.cff b/CITATION.cff
@@ -1,4 +1,4 @@
-cff-version: 0.14.0
+cff-version: 1.0.0
 message: "If you use this software, please cite it as below."
 authors:
   - family-names: "Khider"
@@ -23,8 +23,12 @@ authors:
   - family-names: "McGibbon"
     given-names: "Robert"
     orcid: "https://orcid.org/0000-0003-3337-954X"
+  - family-names: "Voirol"
+    given-names: "Lionel"
+    orcid: "https://orcid.org/0000-0003-1696-1407"
+
 title: "Pyleoclim: A Python package for the analysis and visualization of paleoclimate data"
-version: v0.14.0
+version: v1.0.0
 doi: 10.5281/zenodo.1205661
-date-released: 2024-02-15
+date-released: 2024-06-04
 url: "https://github.com/LinkedEarth/Pyleoclim_util"
diff --git a/doc_build/conf.py b/doc_build/conf.py
@@ -104,14 +104,19 @@
 # The full version, including alpha/beta/rc tags.
 release = pyleo.__version__
 
-
+intersphinx_mapping = {'python': ('https://docs.python.org/3', None),
+                       'numpy': ('https://numpy.org/doc/stable', None),
+                       'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
+                       'pandas': ('https://pandas.pydata.org/pandas-docs/stable', None),
+                       'matplotlib': ('https://matplotlib.org/stable', None)
+                       }
+intersphinx_disabled_reftypes = ["*"]
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -185,7 +190,6 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied

diff --git a/doc_build/rtd_env.yml b/doc_build/rtd_env.yml
@@ -3,14 +3,11 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3.11
+  - python=3.11.0
   - ipykernel
   - pip:
+    - pip
     - cartopy
-    - seaborn
-    - matplotlib
-    - numpy
-    - pandas
     - Sphinx<6.0
     - pylint
     - chardet

diff --git a/environment.yml b/environment.yml
@@ -3,8 +3,9 @@
 name: pyleo
 channels:
   - default
+  - conda-forge
 dependencies:
-  - python>=3.10
+  - python=3.11.0
   - cartopy
   - numba
   - pyyaml

diff --git a/pyleoclim/core/ensemblegeoseries.py b/pyleoclim/core/ensemblegeoseries.py
@@ -281,11 +281,9 @@ def make_labels(self):
         Returns
         -------
         time_header : str
-
             Label for the time axis
 
         value_header : str
-
             Label for the value axis
 
         '''
@@ -318,7 +316,7 @@ def dashboard(self, figsize=[11, 8], gs=None, plt_kwargs=None, histplt_kwargs=No
                   hue='archiveType', marker='archiveType', size=None, scatter_kwargs=None,
                   gridspec_kwargs=None,
                   savefig_settings=None):
-        '''
+        '''Dashboard that plots the trace, histogram, map, and power spectrum of the ensemble.
 
         Parameters
         ----------
@@ -393,7 +391,7 @@ def dashboard(self, figsize=[11, 8], gs=None, plt_kwargs=None, histplt_kwargs=No
 
         See also
         --------
-
+        
         pyleoclim.core.series.Series.plot : plot a timeseries
 
         pyleoclim.core.ensembleseries.EnsembleSeries.plot_envelope: Envelope plots for an ensemble

diff --git a/pyleoclim/core/ensmultivardecomp.py b/pyleoclim/core/ensmultivardecomp.py
@@ -131,27 +131,17 @@ def modeplot(self,index=0,flip=False,plot_envelope_kwargs = None, psd_envelope_k
         
         .. jupyter-execute::
 
-            n = 3 # number of ensembles
-            nn = 30 # number of noise realizations
-            nt = 500
-            ens_list = []
-
-            t,v = pyleo.utils.gen_ts(model='colored_noise',nt=nt,alpha=1.0)
-            signal = pyleo.Series(t,v)
-
-            for _ in range(n): 
-                series_list = []
-                lat = np.random.randint(-90,90)
-                lon = np.random.randint(-180,180)
-                for idx in range(nn):  # noise
-                    noise = np.random.randn(nt,nn)*100
-                    ts = pyleo.GeoSeries(time=signal.time, value=signal.value+noise[:,idx], lat=lat, lon=lon, verbose=False)
-                    series_list.append(ts)
-
-                ts_ens = pyleo.EnsembleSeries(series_list)
-                ens_list.append(ts_ens)
-
-            mul_ens = pyleo.MulEnsGeoSeries([ts_ens])
+            n = 100 # number of series
+
+            soi = pyleo.utils.load_dataset('SOI')
+            soi_time_axes = [pyleo.utils.random_time_axis(n=len(soi.time)) for _ in range(n)]
+            soi_ens = pyleo.EnsembleGeoSeries([pyleo.GeoSeries(time=time, value=soi.value,lat=-5,lon=-85,auto_time_params=True,verbose=False) for time in soi_time_axes])
+
+            nino3 = pyleo.utils.load_dataset('NINO3')
+            nino3_time_axes = [pyleo.utils.random_time_axis(n=len(nino3.time)) for _ in range(n)]
+            nino3_ens = pyleo.EnsembleGeoSeries([pyleo.GeoSeries(time=time, value=nino3.value,lat=-5,lon=-85,auto_time_params=True,verbose=False) for time in nino3_time_axes])
+
+            mul_ens = pyleo.MulEnsGeoSeries([nino3_ens,soi_ens])
             mcpca = mul_ens.mcpca(nsim=10,seed=42)
             mcpca.modeplot()'''
 
@@ -328,27 +318,17 @@ def screeplot(self,clr_eig='C0', linewidth=.3, title='Screeplot', violin_kwargs
         
         .. jupyter-execute::
         
-            n = 3 # number of ensembles
-            nn = 30 # number of noise realizations
-            nt = 500
-            ens_list = []
-
-            t,v = pyleo.utils.gen_ts(model='colored_noise',nt=nt,alpha=1.0)
-            signal = pyleo.Series(t,v)
-
-            for _ in range(n): 
-                series_list = []
-                lat = np.random.randint(-90,90)
-                lon = np.random.randint(-180,180)
-                for idx in range(nn):  # noise
-                    noise = np.random.randn(nt,nn)*100
-                    ts = pyleo.GeoSeries(time=signal.time, value=signal.value+noise[:,idx], lat=lat, lon=lon, verbose=False)
-                    series_list.append(ts)
-
-                ts_ens = pyleo.EnsembleSeries(series_list)
-                ens_list.append(ts_ens)
-
-            mul_ens = pyleo.MulEnsGeoSeries([ts_ens])
+            n = 100 # number of series
+
+            soi = pyleo.utils.load_dataset('SOI')
+            soi_time_axes = [pyleo.utils.random_time_axis(n=len(soi.time)) for _ in range(n)]
+            soi_ens = pyleo.EnsembleGeoSeries([pyleo.GeoSeries(time=time, value=soi.value,lat=0,lon=0,auto_time_params=True,verbose=False) for time in soi_time_axes])
+
+            nino3 = pyleo.utils.load_dataset('NINO3')
+            nino3_time_axes = [pyleo.utils.random_time_axis(n=len(nino3.time)) for _ in range(n)]
+            nino3_ens = pyleo.EnsembleGeoSeries([pyleo.GeoSeries(time=time, value=nino3.value,lat=0,lon=0,auto_time_params=True,verbose=False) for time in nino3_time_axes])
+
+            mul_ens = pyleo.MulEnsGeoSeries([nino3_ens,soi_ens])
             mcpca = mul_ens.mcpca(nsim=10,seed=42)
             mcpca.screeplot()'''
 

diff --git a/pyleoclim/core/multiplegeoseries.py b/pyleoclim/core/multiplegeoseries.py
@@ -82,15 +82,14 @@ def __init__(self, series_list, time_unit=None, label=None):
 
         super().__init__(series_list, time_unit, label)
 
-    # ============ MAP goes here ================
 
     def map(self, marker='archiveType', hue='archiveType', size=None, cmap=None,
             edgecolor='k', projection='auto',
             proj_default=True, crit_dist=5000, colorbar=True,color_scale_type=None,
             background=True, borders=False, coastline=True,rivers=False, lakes=False, land=True,ocean=True,
             figsize=None, fig=None, scatter_kwargs=None, gridspec_kwargs=None, legend=True, gridspec_slot=None,
             lgd_kwargs=None, savefig_settings=None, **kwargs):
-        '''
+        '''Mapping of the collection of GeoSeries objects.
         
 
         Parameters

diff --git a/pyleoclim/core/multipleseries.py b/pyleoclim/core/multipleseries.py
@@ -1932,7 +1932,6 @@ def stripes(self, cmap = 'RdBu_r', sat=1.0, ref_period=None,
         figsize : list
             a list of two integers indicating the figure size (in inches)
         
-        
         sat : float > 0
             Controls the saturation of the colormap normalization by scaling the vmin, vmax in https://matplotlib.org/stable/tutorials/colors/colormapnorms.html
             default = 1.0
@@ -1941,15 +1940,13 @@ def stripes(self, cmap = 'RdBu_r', sat=1.0, ref_period=None,
             flag indicating whether or not the x-axis should be shown (default = False) 
             
         savefig_settings : dictionary
-        
             the dictionary of arguments for plt.savefig(); some notes below:
 
             - 'path' must be specified; it can be any existing or non-existing path,
               with or without a suffix; if the suffix is not given in 'path', it will follow 'format'
             - 'format' can be one of {"pdf", 'eps', 'png', ps'} The default is None.
             
         time_unit : str
-        
             the target time unit, possible inputs:
             {
                 'year', 'years', 'yr', 'yrs',

diff --git a/pyleoclim/core/multivardecomp.py b/pyleoclim/core/multivardecomp.py
@@ -186,12 +186,10 @@ def modeplot(self, index=0, figsize=[8, 8], fig=None, savefig_settings=None,gs=N
                  hue='EOF', marker=None, size=None, scatter_kwargs=None,
                  flip = False, map_kwargs=None, gridspec_kwargs=None):
 
-        ''' Dashboard visualizing the properties of a given mode, including:
-            1. The temporal coefficient (PC or similar)
-            2. its spectrum
-            3. The loadings (EOF or similar), possibly geolocated. If the object
-                does not have geolocation information, a spaghetti plot of the standardized
-                series is displayed.
+        '''Dashboard visualizing the properties of a given mode.
+        
+        Includes: The temporal coefficient (PC or similar), its spectrum, and the loadings (EOF or similar), possibly geolocated. 
+        If the object does not have geolocation information, a spaghetti plot of the standardized series is displayed.
 
         Parameters
         ----------

diff --git a/pyleoclim/core/series.py b/pyleoclim/core/series.py
@@ -457,7 +457,7 @@ def to_csv(self, metadata_header=True, path = None):
         -------
         None
 
-        See Also
+        See also
         --------
 
         pyleoclim.Series.from_csv
@@ -513,7 +513,7 @@ def from_csv(cls, path):
         Series
             pyleoclim Series object containing data and metadata.
 
-        See Also
+        See also
         --------
 
         pyleoclim.Series.to_csv

diff --git a/pyleoclim/utils/causality.py b/pyleoclim/utils/causality.py
@@ -115,24 +115,22 @@ def liang_causality(y1, y2, npt=1, signif_test='isospec', nsim=1000,
     Returns
     -------
     res : dict
-
         A dictionary of results including:
-
-            - T21 : float
-                information flow from y2 to y1 (Note: not y1 -> y2!)
-            - tau21 : float
-                the standardized information flow from y2 to y1
-            - Z : float
-                the total information flow from y2 to y1
-            - dH1_star : float
-                dH*/dt (Liang, 2016)
-            - dH1_noise : float
-            - signif_qs : 
-                the quantiles for significance test
-            - T21_noise : list
-                the quantiles of the information flow from noise2 to noise1 for significance testing
-            - tau21_noise : list
-                the quantiles of the standardized information flow from noise2 to noise1 for significance testing
+        - T21 : float
+            information flow from y2 to y1 (Note: not y1 -> y2!)
+        - tau21 : float
+            the standardized information flow from y2 to y1
+        - Z : float
+            the total information flow from y2 to y1
+        - dH1_star : float
+            dH*/dt (Liang, 2016)
+        - dH1_noise : float
+        - signif_qs :
+            the quantiles for significance test
+        - T21_noise : list
+            the quantiles of the information flow from noise2 to noise1 for significance testing
+        - tau21_noise : list
+            the quantiles of the standardized information flow from noise2 to noise1 for significance testing
     
     See also
     --------
@@ -262,18 +260,13 @@ def liang(y1, y2, npt=1):
     Returns
     -------
     res : dict
-
         A dictionary of results including:
 
-            - T21 : float
-                information flow from y2 to y1 (Note: not y1 -> y2!)
-            - tau21 : float
-                the standardized information flow from y2 to y1
-            - Z : float
-                the total information flow from y2 to y1
-            - dH1_star : float
-                dH*/dt (Liang, 2016)
-            - dH1_noise : float
+            - T21 (float): information flow from y2 to y1 (Note: not y1 -> y2!)
+            - tau21 (float): the standardized information flow from y2 to y1
+            - Z (float): the total information flow from y2 to y1
+            - dH1_star (float): dH*/dt (Liang, 2016)
+            - dH1_noise (float)
             
     See also
     --------
@@ -464,9 +457,7 @@ def signif_isospec(y1, y2, method,
     Returns
     -------
     res_dict : dict
-
         A dictionary with the following information:
-
           - T21_noise_qs : list
                         the quantiles of the information flow from noise2 to noise1 for significance testing
           - tau21_noise_qs : list

diff --git a/setup.py b/setup.py
@@ -2,7 +2,7 @@
 
 from setuptools import setup, find_packages
 
-version = '0.14.1b0'
+version = '1.0.0'
 
 # Read the readme file contents into variable
 def read(fname):
@@ -42,8 +42,9 @@ def read(fname):
         "Unidecode>=1.1.1",
         "cartopy>=0.22.0",
         "pyyaml",
-        "beautifulsoup4", 
-        "scipy", 
+        "beautifulsoup4",
+        "scipy",
+        "requests",
     ],
-    python_requires=">=3.9.0"
+    python_requires=">=3.9",
 )