Merge branch 'Development'

LinkedEarth · Jan 11, 2023 · 8cce337 · 8cce337
2 parents e003cb5 + 82c6c12
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -3,6 +3,7 @@ name: Build container image
 on:
   release:
     branches: [ master ]
+  workflow_dispatch:
 
 jobs:
   build:

diff --git a/.github/workflows/testdev.yml b/.github/workflows/testdev.yml
@@ -9,32 +9,30 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
-    runs-on: ubuntu-20.04
+  test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
 
-    - name: checkout files in repo
-      uses: actions/checkout@v2
+    - name: Checkout files in repo
+      uses: actions/checkout@v3
 
-    - name: Setup Python 3.9
-      uses: actions/setup-python@v2
+    - name: Setup Miniconda
+      uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: 3.9
+        activate-environment: pyleo
+        environment-file: environment.yml
+        python-version: "3.10"
+        auto-activate-base: false
 
-    - name: Install dependencies
+    - name: Conda list
       run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        $CONDA/bin/conda env update --file environment.yml --name base
-
-    - name: Lint with flake
-      run: |
-        $CONDA/bin/conda install flake8
-        # stop the build if there are Python syntax errors or undefined names
-        $CONDA/bin/flake8 . --count --select=E9,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        $CONDA/bin/flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        conda activate pyleo
+        conda list
 
     - name: Test with pytest
       run: |
-        conda install pytest
-        $CONDA/bin/pytest
+        conda activate pyleo
+        pytest pyleoclim/tests -svv
diff --git a/.github/workflows/testmaster.yml b/.github/workflows/testmaster.yml
@@ -9,32 +9,29 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
-    runs-on: ubuntu-20.04
+  test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
 
-    - name: checkout files in repo
-      uses: actions/checkout@v2
+    - name: Checkout files in repo
+      uses: actions/checkout@v3
 
-    - name: Setup Python 3.9
-      uses: actions/setup-python@v2
+    - name: Setup Miniconda
+      uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: 3.9
+        activate-environment: pyleo
+        environment-file: environment.yml
+        python-version: "3.10"
+        auto-activate-base: false
 
-    - name: Install dependencies
+    - name: Conda list
       run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        $CONDA/bin/conda env update --file environment.yml --name base
-
-    - name: Lint with flake
-      run: |
-        $CONDA/bin/conda install flake8
-        # stop the build if there are Python syntax errors or undefined names
-        $CONDA/bin/flake8 . --count --select=E9,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        $CONDA/bin/flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
+        conda activate pyleo
+        conda list
     - name: Test with pytest
       run: |
-        conda install pytest
-        $CONDA/bin/pytest
+        conda activate pyleo
+        pytest pyleoclim/tests -svv
diff --git a/doc_build/anaconda_install.rst b/doc_build/anaconda_install.rst
@@ -4,7 +4,7 @@ Installing Miniconda (Mac, Linux)
 =================================
 
 Anaconda is a very large install, containing not only Python, but also R, and a host of other things that are not necessary to run pyleoclim.
-Users may find it preferable to install the more minimalist "miniconda" package.
+Users may find it preferable to install the minimalist "miniconda" package.
 
 Step 1: Download the installation script for miniconda3
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -42,6 +42,6 @@ Step 3: Test your Installation
 
 .. code-block:: bash
 
-  source ~/.bashrc  # assume you are using Bash shell
+  source ~/.bashrc  # assumes you are using Bash shell
   which python  # should return a path under <base-path>
   which conda  # should return a path under <base-path>
diff --git a/doc_build/citation.rst b/doc_build/citation.rst
@@ -3,7 +3,7 @@
 Citing Pyleoclim
 ================
 
-If Pyleoclim played an important part in your research, please add us to your reference list by using one of the citations below:
+If Pyleoclim played any role in your research, please add us to your reference list by using at least one of the citations below (two if you're really grateful):
 
 BibTeX entry
 """""""""""""
@@ -13,16 +13,26 @@ For example (please check for version updates on Zenodo)
 @misc{Pyleoclim,
    DOI= {10.5281/zenodo.1205661},
    url = {https://doi.org/10.5281/zenodo.1205661},
-   year = {2021},
-   type = {Computer Program}
+   year = {2022},
+   type = {Computer Program},
    title = {Pyleoclim: A Python package for the analysis of paleoclimate data},
    authors = {Deborah Khider and Feng Zhu and Julien Emile-Geay and Jun Hu and Alexander James and Pratheek Athreya and Myron Kwan and Daniel Garijo}
 }
 
 
+@article{Pyleoclim:PP2022,
+	author = {Khider, Deborah and Emile-Geay, Julien and Zhu, Feng and James, Alexander and Landers, Jordan and Ratnakar, Varun and Gil, Yolanda},
+	journal = {Paleoceanography and Paleoclimatology},
+	number = {10},
+	pages = {e2022PA004509},
+	title = {Pyleoclim: Paleoclimate Timeseries Analysis and Visualization With Python},
+	volume = {37},
+	year = {2022},
+  doi = {10.1029/2022PA004509},
+}
+
+
 AGU style entry
 """""""""""""""
 
-Khider, D. et al (2021). Pyleoclim: A Python package for the analysis of paleoclimate data. Retrieved from https://doi.org/10.5281/zenodo.1205661
-
-A manuscript describing Pyleoclim is currently in preprint on the `Earth and Space Science Open Archive <https://www.essoar.org/doi/abs/10.1002/essoar.10511883.1>`_.
+Khider, D., Emile-Geay, J., Zhu, F., James, A., Landers, J., Ratnakar, V., & Gil, Y. (2022). Pyleoclim: Paleoclimate timeseries analysis and visualization with Python. Paleoceanography and Paleoclimatology, 37, e2022PA004509. doi:10.1029/2022PA004509
diff --git a/doc_build/installation.rst b/doc_build/installation.rst
@@ -2,7 +2,7 @@
 
 .. note::
 
-   Pyleoclim requires the use of Python 3.8 or 3.9.
+   Pyleoclim requires the use of Python 3.9 or above
 
 Installing Pyleoclim
 ====================
@@ -20,11 +20,11 @@ Click :ref:`here <anaconda_installation>` for a quick tutorial on MacOs and Linu
 Creating a new conda environment
 """""""""""""""""""""""""""""""""""
 
-To create a new environment using Python 3.9 via command line:
+To create a new environment using Python 3.10 via command line:
 
 .. code-block:: bash
 
-  conda create -n pyleo python=3.9
+  conda create -n pyleo python=3.10
 
 To view a list of available environment:
 
@@ -60,8 +60,9 @@ First install Cartopy:
 
 .. code-block:: bash
 
-  conda install -c conda-forge cartopy
+  conda install -c conda-forge cartopy=0.21
 
+(note: under Python 3.10, cartopy>=0.21 will be installed by default, so specifying this version is unnecessary).
 Then install Pyleoclim through Pypi, which contains the most stable version of Pyleoclim:
 
 .. code-block:: bash
@@ -121,10 +122,18 @@ Again, unless you are planning to make heavy use of the WWZ functionality, we re
 
 Docker Container
 """"""""""""""""
-Docker containers with various versions of Pyleoclim are available at: `https://quay.io/repository/2i2c/paleohack-2021?tab=tags <https://quay.io/repository/2i2c/paleohack-2021?tab=tags>`_.
+Docker containers with various versions of Pyleoclim are available `on quay.io <https://quay.io/repository/linkedearth/pyleoclim?tab=tags>`_.
 
 To pull an image:
 
 .. code-block:: bash
 
-  docker pull quay.io/2i2c/paleohack-2021:latest
+  docker pull quay.io/linkedearth/pyleoclim:latest
+
+To run the image:
+
+.. code-block:: bash
+
+  docker run -it -p 8888:8888 quay.io/linkedearth/pyleoclim:latest
+
+The container will start a Jupyter server automatically. You need to copy the link to the server (localhost) into your web browser on your machine (the command -p 8888:8888 opens the communication port between your machine and the container). You can then create notebook and upload notebook and data using the Jupyter interface. Remember that the container will not save any of your work if you close it. So make sure you donwload your work before closing the container.
diff --git a/doc_build/rtd_env.yml b/doc_build/rtd_env.yml
@@ -3,9 +3,9 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3.9
+  - python=3.10
   - numpy
-  - cartopy>=0.19.0
+  - cartopy=0.21
   - pip:
     - sphinx
     - pylint
@@ -14,4 +14,4 @@ dependencies:
     - nbsphinx
     - IPython
     - readthedocs-sphinx-search>=0.1.0
-    - pyleoclim==0.9.1
+    - git+https://github.com/LinkedEarth/Pyleoclim_util.git@Development
diff --git a/doc_build/savefig/coh.png b/doc_build/savefig/coh.png
diff --git a/doc_build/savefig/mapallarchive.png b/doc_build/savefig/mapallarchive.png
diff --git a/doc_build/savefig/mapallarchive_marker.png b/doc_build/savefig/mapallarchive_marker.png
diff --git a/doc_build/savefig/mapone.png b/doc_build/savefig/mapone.png
diff --git a/doc_build/savefig/mts_stackplot.png b/doc_build/savefig/mts_stackplot.png
diff --git a/doc_build/savefig/random_series.png b/doc_build/savefig/random_series.png
diff --git a/doc_build/savefig/spec_ls.png b/doc_build/savefig/spec_ls.png
diff --git a/doc_build/savefig/spec_ls_freq.png b/doc_build/savefig/spec_ls_freq.png
diff --git a/doc_build/savefig/spec_ls_n50.png b/doc_build/savefig/spec_ls_n50.png
diff --git a/doc_build/savefig/spec_mtm.png b/doc_build/savefig/spec_mtm.png
diff --git a/doc_build/savefig/spec_perio.png b/doc_build/savefig/spec_perio.png
diff --git a/doc_build/savefig/spec_welch.png b/doc_build/savefig/spec_welch.png
diff --git a/doc_build/savefig/spec_wwz.png b/doc_build/savefig/spec_wwz.png
diff --git a/doc_build/savefig/ssa_recon.png b/doc_build/savefig/ssa_recon.png
diff --git a/doc_build/savefig/ts_air.png b/doc_build/savefig/ts_air.png
diff --git a/doc_build/savefig/ts_dashboard.png b/doc_build/savefig/ts_dashboard.png
diff --git a/doc_build/savefig/ts_dist.png b/doc_build/savefig/ts_dist.png
diff --git a/doc_build/savefig/ts_filter1.png b/doc_build/savefig/ts_filter1.png
diff --git a/doc_build/savefig/ts_filter2.png b/doc_build/savefig/ts_filter2.png
diff --git a/doc_build/savefig/ts_filter3.png b/doc_build/savefig/ts_filter3.png
diff --git a/doc_build/savefig/ts_filter4.png b/doc_build/savefig/ts_filter4.png
diff --git a/doc_build/savefig/ts_filter5.png b/doc_build/savefig/ts_filter5.png
diff --git a/doc_build/savefig/ts_nino.png b/doc_build/savefig/ts_nino.png
diff --git a/doc_build/savefig/ts_plot.png b/doc_build/savefig/ts_plot.png
diff --git a/doc_build/savefig/ts_plot2.png b/doc_build/savefig/ts_plot2.png
diff --git a/doc_build/savefig/ts_plot4.png b/doc_build/savefig/ts_plot4.png
diff --git a/doc_build/savefig/ts_plot5.png b/doc_build/savefig/ts_plot5.png
diff --git a/doc_build/savefig/ts_sg.png b/doc_build/savefig/ts_sg.png
diff --git a/doc_build/savefig/wwa_wwz.png b/doc_build/savefig/wwa_wwz.png
diff --git a/doc_build/ts_plot3.png b/doc_build/ts_plot3.png
diff --git a/doc_build/utils/causality.rst b/doc_build/utils/causality.rst
diff --git a/doc_build/utils/correlation.rst b/doc_build/utils/correlation.rst
diff --git a/doc_build/utils/decomposition.rst b/doc_build/utils/decomposition.rst
diff --git a/doc_build/utils/filter.rst b/doc_build/utils/filter.rst
diff --git a/doc_build/utils/introduction.rst b/doc_build/utils/introduction.rst
@@ -14,82 +14,98 @@ to values more appropriate for paleoclimate datasets.
 Causality
 """""""""
 .. automodule:: pyleoclim.utils.causality
-   :members: liang_causality, granger_causality
+  :members:
+  :ignore-module-all: True
+
 
 Correlation
 """""""""""
 
 .. automodule:: pyleoclim.utils.correlation
-   :members: fdr, corr_sig
+  :members:
+  :ignore-module-all: True
 
 Decomposition
 """""""""""""
 
 .. automodule:: pyleoclim.utils.decomposition
-   :members: ssa
+  :members:
+  :ignore-module-all: True
 
 Filter
 """"""
 
 .. automodule:: pyleoclim.utils.filter
-   :members: butterworth, savitzky_golay, firwin, lanczos
+  :members:
+  :ignore-module-all: True
 
 Mapping
 """""""
 
 .. automodule:: pyleoclim.utils.mapping
-   :members: map, compute_distance
+  :members:
+  :ignore-module-all: True
 
 Plotting
 """"""""
 
 .. automodule:: pyleoclim.utils.plotting
-   :members: set_style, closefig, savefig
+  :members:
+  :ignore-module-all: True
 
 Spectral
 """"""""
 
 .. automodule:: pyleoclim.utils.spectral
-   :members: wwz_psd, cwt_psd, mtm, lomb_scargle, welch, periodogram
+  :members:
+  :ignore-module-all: True
+
 
 Tsmodel
 """""""
 
 .. automodule:: pyleoclim.utils.tsmodel
-   :members: ar1_sim, ar1_fit, colored_noise, colored_noise_2regimes, gen_ar1_evenly
+  :members:
+  :ignore-module-all: True
+
 
 
 Wavelet
 """""""
 
 .. automodule:: pyleoclim.utils.wavelet
-   :members: cwt, cwt_coherence, wwz, wwz_coherence
+  :members:
+  :ignore-module-all: True
 
 
 Tsutils
 """""""
 
 .. automodule:: pyleoclim.utils.tsutils
-   :members: simple_stats, bin, interp, gkernel, standardize, ts2segments, annualize, gaussianize, gaussianize_1d, detrend, remove_outliers
+  :members:
+  :ignore-module-all: True
+
 
 
 Tsbase
 """"""
 
 .. automodule:: pyleoclim.utils.tsbase
-   :members: clean_ts, dropna, sort_ts, is_evenly_spaced, reduce_duplicated_timestamps
+  :members:
+  :ignore-module-all: True
+
 
 
 Lipdutils
 """""""""
 
-Utilities to manipulate LiPD files and automate data transformation whenever possible.
-These functions are used throughout Pyleoclim but are not meant for direct interaction by users.
-Also handles integration with the LinkedEarth wiki and the LinkedEarth Ontology.
-
+.. automodule:: pyleoclim.utils.lipdutils
+  :members:
+  :ignore-module-all: True
 
 jsonutils
 """""""""
 
 .. automodule:: pyleoclim.utils.jsonutils
-  :members: PyleoObj_to_json, json_to_PyleoObj, isPyleoclim
+  :members:
+  :ignore-module-all: True
diff --git a/doc_build/utils/jsonutils.rst b/doc_build/utils/jsonutils.rst
diff --git a/doc_build/utils/lipdutils.rst b/doc_build/utils/lipdutils.rst
diff --git a/doc_build/utils/mapping.rst b/doc_build/utils/mapping.rst
diff --git a/doc_build/utils/plotting.rst b/doc_build/utils/plotting.rst
diff --git a/doc_build/utils/spectral.rst b/doc_build/utils/spectral.rst
diff --git a/doc_build/utils/tsbase.rst b/doc_build/utils/tsbase.rst
diff --git a/doc_build/utils/tsmodel.rst b/doc_build/utils/tsmodel.rst
diff --git a/doc_build/utils/tsutils.rst b/doc_build/utils/tsutils.rst
diff --git a/doc_build/utils/wavelet.rst b/doc_build/utils/wavelet.rst
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,6 +3,7 @@ name: Build container image @@
     on:
       release:
         branches: [ master ]
+      workflow_dispatch:
     jobs:
       build:
@@ Expand Down @@