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Fix links #147

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Apr 8, 2024
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11 changes: 11 additions & 0 deletions .github/dependabot.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
# See https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/keeping-your-actions-up-to-date-with-dependabot

version: 2
updates:

- package-ecosystem: "github-actions"
directory: "/"
schedule:
interval: "daily"
labels:
- "Bot"
2 changes: 1 addition & 1 deletion .github/workflows/tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ jobs:
runs-on: ${{ matrix.os }}
strategy:
matrix:
python-version: ["3.8", "3.9", "3.10", "3.11"]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
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os: [windows-latest, ubuntu-latest, macos-latest]
fail-fast: false

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2 changes: 1 addition & 1 deletion docs/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -282,4 +282,4 @@


# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {"https://docs.python.org/": None}
intersphinx_mapping = {"python": ("https://docs.python.org/3", None)}
6 changes: 3 additions & 3 deletions docs/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -119,11 +119,11 @@ Checklist module
Meta
====

* License: MIT, see `LICENSE file <https://github.com/iobis/pyobis/blob/master/LICENSE>`__
* Please note that this project is released with a `Contributor Code of Conduct <https://github.com/iobis/pyobis/blob/master/CONDUCT.md>`__. By participating in this project you agree to abide by its terms.
* License: MIT, see `LICENSE file <https://github.com/iobis/pyobis/blob/main/LICENSE>`__
* Please note that this project is released with a `Contributor Code of Conduct <https://github.com/iobis/pyobis/blob/main/CONDUCT.md>`__. By participating in this project you agree to abide by its terms.

.. |pypi| image:: https://img.shields.io/pypi/v/pyobis.svg
:target: https://pypi.python.org/pypi/pyobis
:target: https://pypi.org/project/pyobis

.. |docs| image:: https://github.com/iobis/pyobis/actions/workflows/deploy-docs.yml/badge.svg
:target: https://iobis.github.io/pyobis
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9,440 changes: 4,724 additions & 4,716 deletions notebooks/usage_guide.ipynb

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6 changes: 3 additions & 3 deletions pyobis/checklist/checklist.py
Original file line number Diff line number Diff line change
Expand Up @@ -132,8 +132,8 @@ def list(
:param geometry: [String] Well Known Text (WKT). A WKT shape written as
either POINT, LINESTRING, LINEARRING
or POLYGON.
Example of a polygon: ((30.1 10.1, 20, 20 40, 40 40, 30.1 10.1)) would
be queried as http://bit.ly/1BzNwDq
Example of a polygon: ((30.1 10.1, 10 20, 20 40, 40 40, 30.1 10.1)) would
be queried as https://api.obis.org/v3/occurrence?geometry=POLYGON%28%2830.1+10.1%2C+10+20%2C+20+40%2C+40+40%2C+30.1+10.1%29%29
:param nodeid: [Fixnum] Node UUID.
:param startdate: [String] Start date YYYY-MM-DD
:param enddate: [String] End date YYYY-MM-DD
Expand All @@ -153,7 +153,7 @@ def list(

# taxonid of 3013
checklist.list(taxonid = 3013).execute()
"""
""" # noqa: E501
url = obis_baseurl + "checklist"
scientificname = handle_arrstr(scientificname)
taxonid = handle_arrint(taxonid)
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8 changes: 4 additions & 4 deletions pyobis/dataset/dataset.py
Original file line number Diff line number Diff line change
Expand Up @@ -34,9 +34,9 @@ def search(
:param geometry: [String] Well Known Text (WKT). A WKT shape written as
either POINT, LINESTRING, LINEARRING
or POLYGON.
Example of a polygon: ((30.1 10.1, 20, 20 40, 40 40, 30.1 10.1)) would
be queried as http://bit.ly/1BzNwDq. Geometry, formatted as WKT or
GeoHash.
Example of a polygon: ((30.1 10.1, 10 20, 20 40, 40 40, 30.1 10.1)) would
be queried as https://api.obis.org/v3/occurrence?geometry=POLYGON%28%2830.1+10.1%2C+10+20%2C+20+40%2C+40+40%2C+30.1+10.1%29%29
Geometry, formatted as WKT or GeoHash.
:param nodeid: [Fixnum] Node UUID.
:param startdate: [Fixnum] Start date
:param enddate: [Boolean] End date
Expand Down Expand Up @@ -91,7 +91,7 @@ def search(

# Get resources for a particular eventDate
data = dataset.search(taxonid=res['worms_id']).execute()
"""
""" # noqa: E501
url = obis_baseurl + "dataset"
scientificname = handle_arrstr(scientificname)
args = {
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6 changes: 3 additions & 3 deletions pyobis/occurrences/occurrences.py
Original file line number Diff line number Diff line change
Expand Up @@ -251,8 +251,8 @@ def search(
:param geometry: [String] Well Known Text (WKT). A WKT shape written
as either POINT, LINESTRING, LINEARRING
or POLYGON.
Example of a polygon: ((30.1 10.1, 20, 20 40, 40 40, 30.1 10.1)) would
be queried as http://bit.ly/1BzNwDq
Example of a polygon: ((30.1 10.1, 10 20, 20 40, 40 40, 30.1 10.1)) would
be queried as https://api.obis.org/v3/occurrence?geometry=POLYGON%28%2830.1+10.1%2C+10+20%2C+20+40%2C+40+40%2C+30.1+10.1%29%29
:param nodeid: [String] Node UUID
:param taxonid: Prev. aphiaid [Fixnum] An Aphia id. This is listed as
the `worms_id` in `taxa`/`taxon` results
Expand Down Expand Up @@ -312,7 +312,7 @@ def search(
occurrences.search(
scientificname="Abra", mof=True, hasextensions="MeasurementOrFact", size=100
).execute()
"""
""" # noqa: E501
url = obis_baseurl + "occurrence"
scientificname = handle_arrstr(scientificname)
taxonid = handle_arrint(taxonid)
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