From d5879a7e8ca70e07ec855c500af5c3866028fb71 Mon Sep 17 00:00:00 2001
From: Ben Armstrong <synrg@debian.org>
Date: Thu, 22 Aug 2024 14:59:24 -0300
Subject: [PATCH] Update to pyinat main HEAD and simplify taxon tree handling.

---
 dronefly/core/formatters/generic.py |  12 +-
 poetry.lock                         | 527 ++++++++++++++--------------
 pyproject.toml                      |   2 +-
 3 files changed, 274 insertions(+), 267 deletions(-)

diff --git a/dronefly/core/formatters/generic.py b/dronefly/core/formatters/generic.py
index c323e95..7da8fdb 100644
--- a/dronefly/core/formatters/generic.py
+++ b/dronefly/core/formatters/generic.py
@@ -198,8 +198,6 @@ def taxa_per_rank(
         _sort_rank_obs_name(order) if sort_by == "obs" else _sort_rank_name(order)
     )
 
-    if not any(taxon.rank in include_ranks for taxon in taxon_list):
-        return []
     tree = make_tree(
         taxon_list,
         include_ranks=include_ranks,
@@ -207,12 +205,6 @@ def taxa_per_rank(
         sort_key=sort_key,
         # max_depth=max_depth,
     )
-    hide_root = (
-        tree.id == ROOT_TAXON_ID
-        or include_ranks
-        and len(include_ranks) == 1
-        and tree.rank != include_ranks[0]
-    )
     root_taxon = None
     if max_depth == 1:
         if root_taxon_id:
@@ -222,7 +214,7 @@ def taxa_per_rank(
             )
         else:
             root_taxon = taxon_list[0]
-    for taxon in tree.flatten(hide_root=hide_root):
+    for taxon in tree.flatten():
         included = True
         # TODO: determine if the taxon is a leaf some other way if the object
         # doesn't have both both a direct & descendant count
@@ -266,7 +258,7 @@ def included_ranks(per_rank: str):
         for rank in COMMON_RANKS:
             ranks += RANKS_FOR_LEVEL[RANK_LEVELS[rank]]
     else:
-        ranks = list(RANK_LEVELS.keys())
+        ranks = [key for key in RANK_LEVELS.keys() if key != "stateofmatter"]
     return ranks
 
 
diff --git a/poetry.lock b/poetry.lock
index c59d8f7..89a4089 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -21,22 +21,22 @@ wrapt = [
 
 [[package]]
 name = "attrs"
-version = "23.2.0"
+version = "24.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
-    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
+    {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"},
+    {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
 ]
 
 [package.extras]
-cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[tests]", "pre-commit"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
-tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
-tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
+benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 
 [[package]]
 name = "backports-tarfile"
@@ -104,33 +104,33 @@ lxml = ["lxml"]
 
 [[package]]
 name = "black"
-version = "24.4.2"
+version = "24.8.0"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -186,63 +186,78 @@ files = [
 
 [[package]]
 name = "cffi"
-version = "1.16.0"
+version = "1.17.0"
 description = "Foreign Function Interface for Python calling C code."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -374,43 +389,38 @@ files = [
 
 [[package]]
 name = "cryptography"
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 optional = false
 python-versions = ">=3.7"
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 ]
 
 [package.dependencies]
@@ -423,7 +433,7 @@ nox = ["nox"]
 pep8test = ["check-sdist", "click", "mypy", "ruff"]
 sdist = ["build"]
 ssh = ["bcrypt (>=3.1.5)"]
-test = ["certifi", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
+test = ["certifi", "cryptography-vectors (==43.0.0)", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
 test-randomorder = ["pytest-randomly"]
 
 [[package]]
@@ -519,13 +529,13 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "8.0.0"
+version = "8.4.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-8.0.0-py3-none-any.whl", hash = "sha256:15584cf2b1bf449d98ff8a6ff1abef57bf20f3ac6454f431736cd3e660921b2f"},
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+    {file = "importlib_metadata-8.4.0-py3-none-any.whl", hash = "sha256:66f342cc6ac9818fc6ff340576acd24d65ba0b3efabb2b4ac08b598965a4a2f1"},
+    {file = "importlib_metadata-8.4.0.tar.gz", hash = "sha256:9a547d3bc3608b025f93d403fdd1aae741c24fbb8314df4b155675742ce303c5"},
 ]
 
 [package.dependencies]
@@ -538,21 +548,25 @@ test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "p
 
 [[package]]
 name = "importlib-resources"
-version = "6.4.0"
+version = "6.4.4"
 description = "Read resources from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "importlib_resources-6.4.4-py3-none-any.whl", hash = "sha256:dda242603d1c9cd836c3368b1174ed74cb4049ecd209e7a1a0104620c18c5c11"},
+    {file = "importlib_resources-6.4.4.tar.gz", hash = "sha256:20600c8b7361938dc0bb2d5ec0297802e575df486f5a544fa414da65e13721f7"},
 ]
 
 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["jaraco.test (>=5.4)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["jaraco.test (>=5.4)", "pytest (>=6,!=8.1.*)", "zipp (>=3.17)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "inflect"
@@ -614,39 +628,39 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-ena
 
 [[package]]
 name = "jaraco-context"
-version = "5.3.0"
+version = "6.0.1"
 description = "Useful decorators and context managers"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jaraco.context-5.3.0-py3-none-any.whl", hash = "sha256:3e16388f7da43d384a1a7cd3452e72e14732ac9fe459678773a3608a812bf266"},
-    {file = "jaraco.context-5.3.0.tar.gz", hash = "sha256:c2f67165ce1f9be20f32f650f25d8edfc1646a8aeee48ae06fb35f90763576d2"},
+    {file = "jaraco.context-6.0.1-py3-none-any.whl", hash = "sha256:f797fc481b490edb305122c9181830a3a5b76d84ef6d1aef2fb9b47ab956f9e4"},
+    {file = "jaraco_context-6.0.1.tar.gz", hash = "sha256:9bae4ea555cf0b14938dc0aee7c9f32ed303aa20a3b73e7dc80111628792d1b3"},
 ]
 
 [package.dependencies]
 "backports.tarfile" = {version = "*", markers = "python_version < \"3.12\""}
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["portend", "pytest (>=6,!=8.1.1)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+test = ["portend", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "jaraco-functools"
-version = "4.0.1"
+version = "4.0.2"
 description = "Functools like those found in stdlib"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jaraco.functools-4.0.1-py3-none-any.whl", hash = "sha256:3b24ccb921d6b593bdceb56ce14799204f473976e2a9d4b15b04d0f2c2326664"},
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+    {file = "jaraco.functools-4.0.2-py3-none-any.whl", hash = "sha256:c9d16a3ed4ccb5a889ad8e0b7a343401ee5b2a71cee6ed192d3f68bc351e94e3"},
+    {file = "jaraco_functools-4.0.2.tar.gz", hash = "sha256:3460c74cd0d32bf82b9576bbb3527c4364d5b27a21f5158a62aed6c4b42e23f5"},
 ]
 
 [package.dependencies]
 more-itertools = "*"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["jaraco.classes", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+test = ["jaraco.classes", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "jeepney"
@@ -665,13 +679,13 @@ trio = ["async_generator", "trio"]
 
 [[package]]
 name = "keyring"
-version = "25.2.1"
+version = "25.3.0"
 description = "Store and access your passwords safely."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -686,8 +700,8 @@ SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""}
 
 [package.extras]
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+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
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 [[package]]
 name = "lazy-object-proxy"
@@ -783,13 +797,13 @@ files = [
 
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+version = "10.4.0"
 description = "More routines for operating on iterables, beyond itertools"
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-python-forge = ">=18.6"
 requests = ">=2.25"
 requests-cache = ">=1.2"
 requests-ratelimiter = ">=0.5.1"
 rich = ">=10.9"
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 [package.extras]
 all = ["filelock (>2.0)", "ujson (>5.0)"]
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+resolved_reference = "8b4f4c6d6b0f7799fcd3663ff2cc3148f34e3b85"
 
 [[package]]
 name = "pylint"
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-testing = ["coverage", "mypy", "pylint", "pytest"]
-
 [[package]]
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 version = "2024.1"
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 ]
 
 [[package]]
@@ -1254,6 +1253,22 @@ files = [
 cryptography = ">=2.0"
 jeepney = ">=0.6"
 
+[[package]]
+name = "setuptools"
+version = "72.2.0"
+description = "Easily download, build, install, upgrade, and uninstall Python packages"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "setuptools-72.2.0-py3-none-any.whl", hash = "sha256:f11dd94b7bae3a156a95ec151f24e4637fb4fa19c878e4d191bfb8b2d82728c4"},
+    {file = "setuptools-72.2.0.tar.gz", hash = "sha256:80aacbf633704e9c8bfa1d99fa5dd4dc59573efcf9e4042c13d3bcef91ac2ef9"},
+]
+
+[package.extras]
+core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.text (>=3.7)", "more-itertools (>=8.8)", "ordered-set (>=3.1.1)", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.11.*)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+
 [[package]]
 name = "six"
 version = "1.16.0"
@@ -1267,13 +1282,13 @@ files = [
 
 [[package]]
 name = "soupsieve"
-version = "2.5"
+version = "2.6"
 description = "A modern CSS selector implementation for Beautiful Soup."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "soupsieve-2.5-py3-none-any.whl", hash = "sha256:eaa337ff55a1579b6549dc679565eac1e3d000563bcb1c8ab0d0fefbc0c2cdc7"},
-    {file = "soupsieve-2.5.tar.gz", hash = "sha256:5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690"},
+    {file = "soupsieve-2.6-py3-none-any.whl", hash = "sha256:e72c4ff06e4fb6e4b5a9f0f55fe6e81514581fca1515028625d0f299c602ccc9"},
+    {file = "soupsieve-2.6.tar.gz", hash = "sha256:e2e68417777af359ec65daac1057404a3c8a5455bb8abc36f1a9866ab1a51abb"},
 ]
 
 [[package]]
@@ -1289,13 +1304,13 @@ files = [
 
 [[package]]
 name = "tomlkit"
-version = "0.13.0"
+version = "0.13.2"
 description = "Style preserving TOML library"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tomlkit-0.13.0-py3-none-any.whl", hash = "sha256:7075d3042d03b80f603482d69bf0c8f345c2b30e41699fd8883227f89972b264"},
-    {file = "tomlkit-0.13.0.tar.gz", hash = "sha256:08ad192699734149f5b97b45f1f18dad7eb1b6d16bc72ad0c2335772650d7b72"},
+    {file = "tomlkit-0.13.2-py3-none-any.whl", hash = "sha256:7a974427f6e119197f670fbbbeae7bef749a6c14e793db934baefc1b5f03efde"},
+    {file = "tomlkit-0.13.2.tar.gz", hash = "sha256:fff5fe59a87295b278abd31bec92c15d9bc4a06885ab12bcea52c71119392e79"},
 ]
 
 [[package]]
@@ -1450,13 +1465,13 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.19.2"
+version = "3.20.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"},
-    {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"},
+    {file = "zipp-3.20.0-py3-none-any.whl", hash = "sha256:58da6168be89f0be59beb194da1250516fdaa062ccebd30127ac65d30045e10d"},
+    {file = "zipp-3.20.0.tar.gz", hash = "sha256:0145e43d89664cfe1a2e533adc75adafed82fe2da404b4bbb6b026c0157bdb31"},
 ]
 
 [package.extras]
@@ -1466,4 +1481,4 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools",
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8.1,<3.13"
-content-hash = "b8fec9b67d04ba338bac6ccee3ace9a4c3d89189bfa2bb86432a5b897f5098d8"
+content-hash = "158fdcea3ec5b2f8da31a3486005418f3985c78d1cdfd43b8801912d2fed87ef"
diff --git a/pyproject.toml b/pyproject.toml
index 58a073b..7903df9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ packages = [
 [tool.poetry.dependencies]
 python = ">=3.8.1,<3.13"
 # pyinaturalist = "=0.20.0.dev0"
-pyinaturalist = { git = "https://github.com/pyinat/pyinaturalist", rev = "12c04689c921a4d2e5cd4352c8e7c525e693b7f0" }
+pyinaturalist = { git = "https://github.com/pyinat/pyinaturalist", rev = "8b4f4c6d6b0f7799fcd3663ff2cc3148f34e3b85" }
 dateparser = "^1.1.1"
 filelock = "^3.13.3"
 inflect = "^5.3.0"