Update docs (#96)

* Automated updating coverage badge * bump to 5.13.1, fix for SSL (#76) * Automated updating coverage badge * `put_description` implemented (#78) * docstring and function signature * function is there and on init - on to tests * tests passing * flake8 pass * updated upload to test pypi to use python 3.8 * adds `get_comment_annotation_ids`, `get_comment_annotation`, `post_comment_annotation` (#79) * added `get_comment_ids` * added `get_comment` * added `post_comment_annotation` * added `test_get_comment_annotation_and_ids` * added `test_post_get_comment_annotation`, all passing * Automated updating coverage badge * fixed typo that set fill color instead of stroke color when stroke not specified (#82) * Automated updating coverage badge * Doi and numpy (#85) * added publication badge * fixed badge * future-proofing against numpy 2.0.0 * added CITATION.cff * Automated updating coverage badge * fixing leftover datasets when `post_dataset` fails to link it to a project (#87) * deleting created dataset if it cannot be linked to project * removed naked except and bad type tests * flake8 * removing print * Automated updating coverage badge * updating omero-py version (#91) * Automated updating coverage badge * changed list of points to be space-separated (#93) * changed list of points to be space-separated * fixing EOL issue * Automated updating coverage badge * `post_file_annotation` can now create orphaned `FileAnnotation`s (#92) * updating omero-py version * post_file_annotation can do orphans * Automated updating coverage badge * updated omero-py version (#94) * updated omero-py version * fix typo in docstring because why not * using glencoe's zeroc-ice * it's installing too fast (!!!) now * Automated updating coverage badge * updated docs --------- Co-authored-by: Erick Ratamero <[email protected]> Co-authored-by: Kiya Govek <[email protected]>
TheJacksonLaboratory · Jan 23, 2024 · cc86237 · cc86237
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diff --git a/.github/workflows/run_tests_pr.yml b/.github/workflows/run_tests_pr.yml
@@ -1,24 +1,24 @@
-name: Run Tests on PR
-on: pull_request
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-      - name: Run docker compose up
-        run: docker-compose -f tests/docker-compose.yml up -d
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install flake8 pytest
-          pip install .[tables]
-      - name: Test with pytest
-        run: |
-          pytest tests/
-
-          
+name: Run Tests on PR
+on: pull_request
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Run docker compose up
+        run: docker-compose -f tests/docker-compose.yml up -d
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest
+          pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20231130/zeroc_ice-3.6.5-cp38-cp38-manylinux_2_28_x86_64.whl
+          pip install .[tables]
+          sleep 60
+      - name: Test with pytest
+        run: |
+          pytest tests/
diff --git a/.github/workflows/run_tests_push.yml b/.github/workflows/run_tests_push.yml
@@ -1,35 +1,37 @@
-name: Run Tests on push
-on: 
-  push:
-    branches: [ main ]
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-      - name: Run docker compose up
-        run: docker-compose -f tests/docker-compose.yml up -d
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install flake8 pytest
-          pip install .[tables]
-      - name: Test with pytest and generate coverage report/badge
-        run: |
-          pip install coverage coverage-badge
-          coverage run -m pytest tests/
-          coverage report -i
-          coverage-badge -f -o coverage.svg
-      - name: Commit badge
-        run: |
-          git config --global user.name 'Erick Ratamero'
-          git config --global user.email '[email protected]'
-          git add coverage.svg
-          git commit --allow-empty -am "Automated updating coverage badge"
-          git push
-
+name: Run Tests on push
+on: 
+  push:
+    branches: [ main ]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Run docker compose up
+        run: docker-compose -f tests/docker-compose.yml up -d
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest
+          pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20231130/zeroc_ice-3.6.5-cp38-cp38-manylinux_2_28_x86_64.whl
+          pip install .[tables]
+          sleep 60
+      - name: Test with pytest and generate coverage report/badge
+        run: |
+          pip install coverage coverage-badge
+          coverage run -m pytest tests/
+          coverage report -i
+          coverage-badge -f -o coverage.svg
+      - name: Commit badge
+        run: |
+          git config --global user.name 'Erick Ratamero'
+          git config --global user.email '[email protected]'
+          git add coverage.svg
+          git commit --allow-empty -am "Automated updating coverage badge"
+          git push
+
diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,80 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: ezomero
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Erick
+    orcid: 'https://orcid.org/0000-0002-7545-3675'
+    family-names: Martins Ratamero
+    affiliation: The Jackson Laboratory
+  - given-names: Kiya
+    family-names: Govek
+    affiliation: The Jackson Laboratory
+    orcid: 'https://orcid.org/0000-0002-2105-0715'
+  - given-names: Julio
+    family-names: Mateos-Langerak
+    affiliation: 'University of Montpellier, CNRS, INSERM'
+    orcid: 'https://orcid.org/0000-0003-1579-0773'
+  - given-names: Fernando
+    family-names: Cervantes Sanchez
+    affiliation: The Jackson Laboratory
+    orcid: 'https://orcid.org/0000-0003-0652-2750'
+  - given-names: David
+    family-names: Mellert
+    affiliation: The Jackson Laboratory
+    orcid: 'https://orcid.org/0000-0001-6606-0274'
+repository-code: 'https://github.com/TheJacksonLaboratory/ezomero'
+abstract: >-
+  Many research laboratories need to manage, process, and
+  analyze the increasingly large volumes and complexity of
+  data being produced by state-of-the-art bioimaging
+  platforms. OMERO is a popular open-source client-server
+  application that provides a unified interface for managing
+  and working with bioimages and their associated
+  measurements and metadata. Integrating OMERO into analysis
+  pipelines, such as those developed around the scientific
+  Python ecosystem, will thus be a common pattern across the
+  field of bioimaging. While OMERO has a powerful Python
+  API, it provides minimal abstraction from the underlying
+  OMERO object model and associated methods, which represent
+  more complexity than most users are interested in for the
+  context of an analysis script. We introduce ezomero, which
+  was designed to provide a convenience layer on top of
+  existing OMERO APIs and return data types that are either
+  Python primitive or commonly used in scientific Python.
+  Ezomero has minimal dependencies in addition to the OMERO
+  Python library itself and is installable directly from
+  PyPI. Here, we provide an overview of ezomero as well as
+  several vignettes to illustrate how it can be used to
+  accelerate discovery.
+license: GPL-2.0
+preferred-citation:
+  type: article
+  authors:
+  - given-names: Erick
+    orcid: 'https://orcid.org/0000-0002-7545-3675'
+    family-names: Martins Ratamero
+    affiliation: The Jackson Laboratory
+  - given-names: Kiya
+    family-names: Govek
+    affiliation: The Jackson Laboratory
+    orcid: 'https://orcid.org/0000-0002-2105-0715'
+  - given-names: Julio
+    family-names: Mateos-Langerak
+    affiliation: 'University of Montpellier, CNRS, INSERM'
+    orcid: 'https://orcid.org/0000-0003-1579-0773'
+  - given-names: Fernando
+    family-names: Cervantes Sanchez
+    affiliation: The Jackson Laboratory
+    orcid: 'https://orcid.org/0000-0003-0652-2750'
+  - given-names: David
+    family-names: Mellert
+    affiliation: The Jackson Laboratory
+    orcid: 'https://orcid.org/0000-0001-6606-0274'
+  title: "Easing OMERO adoption with ezomero"
+  doi: 10.1101/2023.06.29.546930
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-![Run Tests](https://github.com/TheJacksonLaboratory/ezomero/workflows/Run%20Tests/badge.svg?event=push) ![](https://raw.githubusercontent.com/TheJacksonLaboratory/ezomero/main/coverage.svg)
+![](https://raw.githubusercontent.com/TheJacksonLaboratory/ezomero/main/coverage.svg) [![badge-doi](https://img.shields.io/badge/doi-10.1101%2F2023.06.29.546930-purple)](https://doi.org/10.1101/2023.06.29.546930) 
 
 # ezomero
 A module with convenience functions for writing Python code that interacts with OMERO.

diff --git a/docs/.buildinfo b/docs/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
 config: 7a4479f70573ca754fdc70b0d9982900
-tags: 645f666f9bcd5a90fca523b33c5a78b7
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/.doctrees/ezomero.doctree b/docs/.doctrees/ezomero.doctree
diff --git a/docs/_sources/ezomero.rst.txt b/docs/_sources/ezomero.rst.txt
@@ -1,29 +1,29 @@
-ezomero package
-===============
-
-Submodules
-----------
-
-ezomero.json\_api module
-------------------------
-
-.. automodule:: ezomero.json_api
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-ezomero.rois module
--------------------
-
-.. automodule:: ezomero.rois
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: ezomero
-   :members:
-   :undoc-members:
-   :show-inheritance:
+ezomero package
+===============
+
+Submodules
+----------
+
+ezomero.json\_api module
+------------------------
+
+.. automodule:: ezomero.json_api
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ezomero.rois module
+-------------------
+
+.. automodule:: ezomero.rois
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: ezomero
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_sources/modules.rst.txt b/docs/_sources/modules.rst.txt
@@ -1,7 +1,7 @@
-ezomero
-=======
-
-.. toctree::
-   :maxdepth: 4
-
-   ezomero
+ezomero
+=======
+
+.. toctree::
+   :maxdepth: 4
+
+   ezomero