Merge pull request #12 from chenyangkang/chenyangkang-JOSS-review

add pre-commit

.gitattributes

@@ -1,4 +1,3 @@
 *.ipynb linguist-vendored
 *.md linguist-vendored
 *.bib linguist-vendored
-

.github/workflows/compile_docs.yml

@@ -1,9 +1,9 @@
-name: compile_docs 
+name: compile_docs
 
 on:
   push:
-    paths:
-      - 'docs/**'
+    # paths:
+    #   - 'docs/**'
     branches:
       - main
 

.github/workflows/draft-pdf.yml

@@ -31,4 +31,4 @@ jobs:
       # - name: save pdf to repo
       #   uses: chenyangkang/git-auto-commit-action@v4
       #   with:
-      #     commit_message: Saved new PDF of paper
+      #     commit_message: Saved new PDF of paper

.github/workflows/publish-pypi.yml

@@ -0,0 +1,39 @@
+# name: publish-pypi
+# on:
+#   push:
+#     paths:
+#       - 'stemflow/version.py'
+#     tags:
+#       - "v*.*.*.*"
+
+# jobs:
+#   publish:
+#     runs-on: ubuntu-latest
+#     environment:
+#       name: pypi
+#       url: https://pypi.org/p/stemflow/
+#     permissions:
+#       id-token: write
+#     steps:
+#       - uses: actions/checkout@v4
+#       - name: Python setup
+#         uses: actions/setup-python@v5
+#         with:
+#           python-version: 3.9
+#           cache: 'pip'
+#       - name: Install package
+#         run: |
+#           python -m pip install --upgrade pip
+#           pip install wheel
+#           pip install .
+#       - name: Build package
+#         run: |
+#           python setup.py sdist bdist_wheel
+#       - name: Publish to PyPI
+#         uses: pypa/gh-action-pypi-publish@release/v1
+#         with:
+#           user: __token__
+#           password: ${{ secrets.PYPI_API_TOKEN }}
+#           packages_dir: ./dist
+#           # repository-url: https://pypi.org/p/stemflow/
+#           verbose: true

.github/workflows/run_pytest.yml

@@ -35,7 +35,7 @@ jobs:
       uses: codecov/codecov-action@v3
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-        
+
     # - uses: action-badges/create-orphan-branch@0.1.0
     #   with:
     #     branch-name: badges
@@ -46,4 +46,4 @@ jobs:
     #     file-name: coverage.svg
     #     badge-branch: badges
     #     github-token: '${{ secrets.SECRET_TOKEN }}'
-    #     coverage-file-name: ./coverage.xml
+    #     coverage-file-name: ./coverage.xml

.pre-commit-config.yaml

@@ -0,0 +1,32 @@
+# default_language_version:
+#   python: python3.8
+
+repos:
+  - repo: https://github.com/ambv/black
+    rev: 23.1.0
+    hooks:
+      - id: black
+        args: ["stemflow", "--line-length=120", "--target-version=py37"]
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        args: ["--select=C,E,F,W,B,B950", "--max-line-length=120", "--ignore=E203,E501,W503,F401,F403"]
+
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["-l 120", "--profile", "black", "."]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-yaml
+        exclude: recipe/meta.yaml
+      - id: check-added-large-files
+        args: ["--maxkb=1024"]
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: requirements-txt-fixer

LICENSE

@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.

docs/API_Documentation/stemflow.mini_test.md

@@ -1,3 +1,3 @@
 # stemflow.mini_test
 
-::: stemflow.mini_test
+::: stemflow.mini_test

docs/API_Documentation/stemflow.model.Hurdle.md

@@ -2,4 +2,4 @@
 
 ---
 :::stemflow.model.Hurdle
----
+---

docs/API_Documentation/stemflow.model.dummy_model.md

@@ -2,4 +2,4 @@
 
 ---
 :::stemflow.model.dummy_model
----
+---

docs/API_Documentation/stemflow.model.special_hurdle.md

@@ -2,4 +2,4 @@
 
 ---
 :::stemflow.model.special_hurdle
----
+---

docs/API_Documentation/stemflow.model_selection.md

@@ -1,3 +1,3 @@
 # stemflow.model_selection
 
-::: stemflow.model_selection
+::: stemflow.model_selection

docs/API_Documentation/stemflow.utils.generate_soft_colors.md

@@ -1,3 +1,3 @@
 # stemflow.utils.generate_soft_colors
 
-:::stemflow.utils.generate_soft_colors
+:::stemflow.utils.generate_soft_colors

docs/API_Documentation/stemflow.utils.plot_gif.md

@@ -2,4 +2,4 @@
 
 ---
 :::stemflow.utils.plot_gif
----
+---

docs/API_Documentation/stemflow.utils.quadtree.md

@@ -2,4 +2,4 @@
 
 ---
 :::stemflow.utils.quadtree
----
+---

docs/CONTRIBUTING.md

@@ -27,6 +27,3 @@ git remote add upstream git://github.com/stemflow/stemflow.git
 This creates the directory `stemflow-YOURNAME` and connects your repository to the upstream (main project) elapid repository.
 
 ---
-
-
-

docs/Fun_Visualization/Global_Bird_Shannon_H_Index.md

@@ -4,6 +4,3 @@ Data Source: eBird
 
 
 ![](./shannon_H_2020.gif)
-
-
-

docs/Fun_Visualization/Global_Mean_Temperature_2020.md

@@ -6,7 +6,3 @@ Notice: the visualized data is not modeled by AdaSTEM. Only visualization functi
 
 
 ![](./Temp_2020.gif)
-
-
-
-

docs/Fun_Visualization/Global_NDVI.md

@@ -6,6 +6,3 @@ Notice: the visualized data is not modeled by AdaSTEM. Only visualization functi
 
 
 ![](./NDVI_2020.gif)
-
-
-

docs/Fun_Visualization/Ruby-crowned_Kinglet_2020.md

@@ -6,5 +6,3 @@ Data Source: eBird
 ![](./Ruby-crowned_Kinglet_2020.gif)
 
 It's quite amazing that the Ruby-crowned_Kinglet gathered for wintering and spread into two distinct populations during the breeding season.
-
-

docs/css/extra.css

@@ -21,4 +21,4 @@
     .md-content {
       margin-right: 0;
     }
-  } */
+  } */

docs/index.md

@@ -13,9 +13,10 @@
 ![PyPI version](https://img.shields.io/pypi/v/stemflow)
 ![PyPI downloads](https://img.shields.io/pypi/dm/stemflow)
 ![GitHub last commit](https://img.shields.io/github/last-commit/chenyangkang/stemflow)
+[![codecov](https://codecov.io/gh/chenyangkang/stemflow/graph/badge.svg?token=RURPF6NKIJ)](https://codecov.io/gh/chenyangkang/stemflow)
 [![status](https://joss.theoj.org/papers/50a385b3283faf346fc16484f50f6add/status.svg)](https://joss.theoj.org/papers/50a385b3283faf346fc16484f50f6add)
  <!--  -->
- 
+
 -----
 
 ## Documentation :book:
@@ -68,22 +69,22 @@ model = AdaSTEMRegressor(
         regressor=XGBRegressor(tree_method='hist',random_state=42, verbosity = 0, n_jobs=1)
     ),
     save_gridding_plot = True,
-    ensemble_fold=10, 
+    ensemble_fold=10,
     min_ensemble_required=7,
     grid_len_lon_upper_threshold=25,
     grid_len_lon_lower_threshold=5,
     grid_len_lat_upper_threshold=25,
     grid_len_lat_lower_threshold=5,
-    temporal_start = 1, 
+    temporal_start = 1,
     temporal_end =366,
     temporal_step=20,
     temporal_bin_interval = 50,
     points_lower_threshold=50,
     Spatio1='longitude',
-    Spatio2 = 'latitude', 
+    Spatio2 = 'latitude',
     Temporal1 = 'DOY',
     use_temporal_to_train=True,
-    njobs=1                       
+    njobs=1
 )
 ```
 
@@ -119,7 +120,7 @@ model.gridding_plot
 
 Here, each color shows an ensemble generated during model fitting. In each of the 10 ensembles, regions (in terms of space and time) with more training samples were gridded into finer resolution, while the sparse one remained coarse. Prediction results were aggregated across the ensembles (that is, in this example, data were modeled 10 times).
 
----- 
+----
 ## Example of visualization :world_map:
 
 Daily Abundance Map of Barn Swallow

mkdocs.yml

@@ -69,7 +69,7 @@ extra:
     # - icon: fontawesome/brands/linkedin
     #   link: https://www.linkedin.com/in/willettjames/
 
-    
+
 nav:
   - Home: index.md
   - Examples:
@@ -119,9 +119,9 @@ markdown_extensions:
   - pymdownx.superfences
   - pymdownx.mark
   - attr_list
-  - pymdownx.emoji:
-      emoji_index: !!python/name:materialx.emoji.twemoji
-      emoji_generator: !!python/name:materialx.emoji.to_svg
+  - pymdownx.emoji
+      # emoji_index: !!python/name:materialx.emoji.twemoji
+      # emoji_generator: !!python/name:materialx.emoji.to_svg
   - pymdownx.critic
   - pymdownx.caret
   - pymdownx.keys
@@ -132,4 +132,4 @@ extra_css:
 
 
 copyright: |
-  &copy; 2023 <a href="https://github.com/chenyangkang"  target="_blank" rel="noopener">Yangkang Chen</a>
+  &copy; 2023 <a href="https://github.com/chenyangkang"  target="_blank" rel="noopener">Yangkang Chen</a>

paper/md_paper/paper.bib

@@ -422,7 +422,3 @@ @article{a_leeyaw_species_2022
 	pages = {e05877},
 	file = {A. Lee‐Yaw et al. - 2022 - Species distribution models rarely predict the bio.pdf:/Users/chenyangkang/Zotero/storage/47MPKJDC/A. Lee‐Yaw et al. - 2022 - Species distribution models rarely predict the bio.pdf:application/pdf},
 }
-
-
-
-

paper/md_paper/paper.md

@@ -11,7 +11,7 @@ authors:
  - given-names: Yangkang
    surname: Chen
    orchid: 0000-0003-4996-0881
-   affiliation: "1, 2" 
+   affiliation: "1, 2"
  - given-names: Zhongru
    surname: Gu
    orchid: 0000-0002-0178-1107
@@ -31,7 +31,7 @@ affiliations:
 
  - name: Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
    index: 3
-   
+
  - name: Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
    index: 4
 
@@ -65,4 +65,4 @@ While there exists mounting open source packages for species distribution modeli
 
 This project was based upon work supported by National Natural Science Foundation of China grants 32125005 (to X.Z.), 32270455 (to Z.G.), CAS Project for Young Scientists in Basic Research (YSBR-097 to X.Z. and Z.G.). We thank Dr. Daniel Fink at Cornell Lab of Ornithology for the R scripts of STEM model and QuadTree which inspired our implementation in Python.
 
-# References
+# References