Metadata-Version: 2.1
Name: pyinaturalist
Version: 0.11.0
Summary: Python client for the iNaturalist APIs
Home-page: https://github.com/niconoe/pyinaturalist
Author: Nicolas Noé
Author-email: nicolas@niconoe.eu
License: MIT license
Description: # pyinaturalist
        
        
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        Python client for the [iNaturalist APIs](https://www.inaturalist.org/pages/api+reference).
        See full documentation at https://pyinaturalist.readthedocs.io.
        
        ## Installation
        
        Install the latest stable version with pip:
        
        ```bash
        $ pip install pyinaturalist
        ```
        
        Or, if you would like to use the latest development (non-stable) version:
        
        ```bash
        $ pip install --pre pyinaturalist
        ```
        
        To set up for local development (preferably in a new virtualenv):
        
        ```bash
        $ git clone https://github.com/niconoe/pyinaturalist.git
        $ cd pyinaturalist
        $ pip install -Ue ".[dev]"
        ```
        
        ## Development Status
        
        Pyinaturalist is under active development. Currently, a handful of the most relevant API endpoints
        are implemented, including:
        
        * Searching, creating, and updating observations and observation fields
        * Searching for places, projects, species, and species counts
        * Text search autocompletion for species and places
        
        See below for some examples,
        see [Endpoints](https://pyinaturalist.readthedocs.io/en/latest/endpoints.html) for a complete list of implemented endpoints, and
        see [Issues](https://github.com/niconoe/pyinaturalist/issues) for planned & proposed features.
        
        More endpoints will continue to be added as they are needed.
        Please **create an issue** if there is an endpoint you would like to have added, and **PRs are welcome!**
        
        **Note:**
        
        The two iNaturalist APIs expose a combined total of 103 endpoints\*. Some of these are generally
        useful and could potentially be added to pyinaturalist, but many others are primarily for
        internal use by the iNaturalist web application and mobile apps, and are unlikely to be added
        unless there are specific use cases for them.
        
        \*As of 2020-10-01: 37 in REST API, 65 in Node API, and 1 undocumented 
        
        ## Examples
        
        ### Observations
        
        #### Search observations
        
        ```python
        from pyinaturalist.node_api import get_all_observations
        obs = get_all_observations(user_id='my_username')
        ```
        
        See [available parameters](https://api.inaturalist.org/v1/docs/#!/Observations/get_observations/)
        
        #### Get an access token
        
        For authenticated API calls (creating/updating/deleting data), you first need to obtain an access token.
        This requires creating an [iNaturalist app](https://www.inaturalist.org/oauth/applications/new).
        
        ```python
        from pyinaturalist.rest_api import get_access_token
        token = get_access_token(
            username='<your_inaturalist_username>',
            password='<your_inaturalist_password>',
            app_id='<your_inaturalist_app_id>',
            app_secret='<your_inaturalist_app_secret>',
        )
        ```
        
        #### Create a new observation
        ```python
        from pyinaturalist.rest_api import create_observation
        from datetime import datetime
        
        response = create_observation(
            taxon_id=54327,  # Vespa Crabro
            observed_on_string=datetime.now().isoformat(),
            time_zone='Brussels',
            description='This is a free text comment for the observation',
            tag_list='wasp, Belgium',
            latitude=50.647143,
            longitude=4.360216,
            positional_accuracy=50, # meters,
            # sets vespawatch_id (an observation field whose ID is 9613) to the value '100'.
            observation_field_values_attributes=[
                {'observation_field_id': 9613,'value': 100},
            ],
            access_token=token,
        )
        new_observation_id = response[0]['id']
        ```
        
        #### Upload a picture for this observation
        ```python
        from pyinaturalist.rest_api import add_photo_to_observation
        
        r = add_photo_to_observation(
            new_observation_id,
            access_token=token,
            photo='/Users/nicolasnoe/vespa.jpg',
        )
        ```
        
        #### Update an existing observation of yours
        ```python
        from pyinaturalist.rest_api import update_observation
        
        r = update_observation(
            17932425,
            access_token=token,
            description='updated description !',
        )
        ```
        
        #### Get a list of all (globally available) observation fields
        ```python
        from pyinaturalist.rest_api import get_all_observation_fields
        r = get_all_observation_fields(search_query="DNA")
        ```
        
        #### Set an observation field value on an existing observation
        ```python
        from pyinaturalist.rest_api import put_observation_field_values
        
        put_observation_field_values(
            observation_id=7345179,
            observation_field_id=9613,
            value=250,
            access_token=token,
        )
        ```
        
        #### Get observation data in alternative formats
        A separate endpoint can provide other data formats, including Darwin Core, KML, and CSV:
        
        ```python
        from pyinaturalist.rest_api import get_observations
        obs = get_observations(user_id='niconoe', response_format='dwc')
        ```
        
        See [available parameters and formats](https://www.inaturalist.org/pages/api+reference#get-observations)
        
        #### Get observation species counts
        There is an additional endpoint to get counts of observations by species.
        On the iNaturalist web UI, this information can be found on the 'Species' tab of search results.
        For example, to get the counts of all your own research-grade observations:
        
        ```python
        from pyinaturalist.node_api import get_observation_species_counts
        obs_counts = get_observation_species_counts(user_id='my_username', quality_grade='research')
        ```
        
        ### Taxonomy
        
        #### Search species and other taxa
        Let's say you partially remember either a genus or family name that started with **'vespi'**-something:
        
        ```python
        >>> from pyinaturalist.node_api import get_taxa
        >>>
        >>> response = get_taxa(q="vespi", rank=["genus", "family"])
        >>> print({taxon["id"]: taxon["name"] for taxon in response["results"]})
        {52747: "Vespidae", 84737: "Vespina", 92786: "Vespicula", 646195: "Vespiodes", ...}
        ```
        
        Oh, that's right, it was **'Vespidae'**! Now let's find all of its subfamilies using its taxon ID
        from the results above:
        
        ```python
        >>> response = get_taxa(parent_id=52747)
        >>> print({taxon["id"]: taxon["name"] for taxon in response["results"]})
        {343248: "Polistinae", 84738: "Vespinae", 119344: "Eumeninae", 121511: "Masarinae", ...}
        ```
        
        ### Get a species by ID
        Let's find out more about this 'Polistinae' genus. We could search for it by name or by ID,
        but since we already know the ID from the previous search, let's use that:
        
        ```python
        >>> from pyinaturalist.node_api import get_taxa_by_id
        >>> response = get_taxa_by_id(343248)
        ```
        
        There is a lot of info in there, but let's just get the basics for now:
        
        ```python
        >>> basic_fields = ["preferred_common_name", "observations_count", "wikipedia_url", "wikipedia_summary"]
        >>> print({f: response["results"][0][f] for f in basic_fields})
        {
            "preferred_common_name": "Paper Wasps",
            "observations_count": 69728,
            "wikipedia_url": "http://en.wikipedia.org/wiki/Polistinae",
            "wikipedia_summary": "The Polistinae are eusocial wasps closely related to the more familiar yellow jackets...",
        }
        ```
        
        #### Taxon autocomplete
        This is a text search-optimized endpoint that provides autocompletion in the Naturalist web UI:
        
        ![Taxon autocompletion in the iNaturalist web UI](docs/images/taxon_autocomplete.png)
        
        This one is a bit more niche, but it provides a fast way to search the iNaturalist taxonomy
        database. Here is an example that will run searches from console input:
        
        ```python
        from pyinaturalist.node_api import get_taxa_autocomplete
        
        while True:
            query = input("> ")
            response = get_taxa_autocomplete(q=query, minify=True)
            print("\n".join(response["results"]))
        ```
        
        Example usage:
        
        ```
        > opilio
        527573:     Genus Opilio
        47367:      Order Opiliones (Harvestmen)
        84644:      Species Phalangium opilio (European Harvestman)
        527419:     Subfamily Opilioninae
        ...
        > coleo
        372759:     Subclass Coleoidea (Coleoids)
        47208:      Order Coleoptera (Beetles)
        359229:     Species Coleotechnites florae (Coleotechnites Flower Moth)
        53502:      Genus Brickellia (brickellbushes)
        ...
        <Ctrl-C>
        ```
        
        If you get unexpected matches, the search likely matched a synonym, either in the form of a
        common name or an alternative classification. Check the `matched_term` property for more
        info. For example:
        
        ```python
        >>> first_result = get_taxa_autocomplete(q='zygoca')['results'][0]
        >>> first_result["name"]
        "Schlumbergera truncata"
        >>> first_result["matched_term"]
        "Zygocactus truncatus"  # An older synonym for Schlumbergera
        ```
        
        # History
        
        ## 0.11.0 (2020-11-04)
        [See all Issues & PRs](https://github.com/niconoe/pyinaturalist/milestone/2?closed=1)
        
        ### New Endpoints
        * Added new functions for Node API **Places** endpoints:
            * `get_places_by_id()`
            * `get_places_nearby()`
            * `get_places_autocomplete()`
        * Added new functions for Node API **Projects** endpoints:
            * `get_projects()`
            * `get_projects_by_id()`
        * Added new function for an additional Node API **Observation** endpoint:
            * `get_observation_species_counts()`
            * `get_all_observation_species_counts()`
        
        ### Modified Endpoints
        * Added support for simplified observation field syntax (`observation_fields={id: value}`)
          for `create_observations()` and `update_observation()`
        * Updated `node_api.get_taxa_by_id()` to accept multiple IDs
        * Updated `rest_api.get_observations()` with type conversion from strings to floats for response lat/long coordinates.
          Only applies to JSON response format.
        * Updated `node_api.get_taxa_autocomplete()` with optional `min_rank` and `max_rank` parameters, for consistency with `get_taxa()`
        * Using the `params` positional argument for the handful of functions that used it
          will raise a `DeprecationWarning`, but will otherwise still be functional until `0.12`
        * Renamed `search_query` argument to `q` to be consistent with API request parameters
        * Using the `search_query` argument for `rest_api.get_observation_fields()` and `rest_api.get_all_observation_fields()`
          will raise a `DeprecationWarning`, but will otherwise still be functional until `0.12`
        * Renamed `create_observations()` to `create_observation()`, as this only supports creating a single observation per
          call. This is aliased to `create_observations()` for backwards-compatibility, but will raise a `DeprecationWarning`.
        
        ### Documentation & Usability
        * Added example response data to docs all endpoints
        * Added links to official API reference to docs for all endpoints
        * Added full API request parameters to all API functions, in the form of keyword arguments with type annotations and docstrings
        * Added complete table of iNaturalist API endpoints and endpoints implemented by pyinaturalist
        * Added and improved usage examples
        * Numerous other documentation improvements
        * Made all API function signatures consistent by taking request params as keyword arguments
        
        ### Other Changes
        * Dropped testing & support for python 3.4
        * Added testing & support for python 3.9
        * Added parameter validation for multiple-choice request parameters
        
        ## 0.10.0 (2020-06-16)
        [See all Issues & PRs](https://github.com/niconoe/pyinaturalist/milestone/1?closed=1)
        
        ### New Endpoints
        * Added new **Observation** endpoint: `rest_api.get_observations()`, with 6 additional observation response formats, including GeoJSON, Darwin Core, and others
        
        ### Modified Endpoints
        * Added `minify` option to `node_api.get_taxa_autocomplete()`
        
        ### Other Changes
        * Added more info & examples to README for taxa endpoints, and other documentation improvements
        * Added conversion for all date and datetime parameters to timezone-aware ISO 8601 timestamps
        * Added a dry-run mode to mock out API requests for testing
        * Set up pre-release builds for latest development version
        
        ## 0.9.1 (2020-05-26)
        
        * Bugfix: proper support for boolean and integer list parameters (see https://github.com/niconoe/pyinaturalist/issues/17).
        
        ## 0.9.0 (2020-05-06)
        
        ### New Endpoints
        * Added new functions for Node API **Taxa** endpoints:
        
            * `node_api.get_taxa()`
            * `node_api.get_taxa_autocomplete()`
            * `node_api.get_taxa_by_id()`
        
        ## 0.8.0 (2019-07-11)
        
        * All functions now take an optional `user-agent <https://en.wikipedia.org/wiki/User_agent>`_ parameter in order to identify yourself to iNaturalist. If not set, `Pyinaturalist/<VERSION>` will be used.
        
        ## 0.7.0 (2019-05-08)
        
        * `rest_api.delete_observation()` now raises `ObservationNotFound` if the observation doesn't exist
        * minor dependencies update for security reasons
        
        ## 0.6.0 (2018-11-15)
        
        * New function: `rest_api.delete_observation()`
        
        ## 0.5.0 (2018-11-05)
        
        * New function: `node_api.get_observation()`
        
        ## 0.4.0 (2018-11-05)
        
        * `create_observation()` now raises exceptions in case of errors.
        
        ## 0.3.0 (2018-11-05)
        
        * `update_observation()` now raises exceptions in case of errors.
        
        ## 0.2.0 (2018-10-31)
        
        * Better infrastructure (type annotations, documentation, ...)
        * Dropped support for Python 2.
        * New function: `update_observation()`
        * `rest_api.AuthenticationError` is now `exceptions.AuthenticationError`
        
        ## 0.1.0 (2018-10-10)
        
        * First release on PyPI.
        
Keywords: pyinaturalist,iNaturalist
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Description-Content-Type: text/markdown
Provides-Extra: build
Provides-Extra: docs
Provides-Extra: test
Provides-Extra: dev
