From 1aed7a029f187e0bb35c559b5a5e1b19cd336dfe Mon Sep 17 00:00:00 2001
From: Luchesar ILIEV <luchesar.iliev@gmail.com>
Date: Tue, 26 Nov 2024 15:21:56 +0200
Subject: [PATCH 1/6] deps: update; pin h5pyd, pynanomapper, ramanchada2

---
 poetry.lock    | 2114 ++++++++++++++++++++++++------------------------
 pyproject.toml |    7 +-
 2 files changed, 1070 insertions(+), 1051 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 7132a73..ba4d7a9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand.
 
 [[package]]
 name = "annotated-types"
@@ -13,13 +13,13 @@ files = [
 
 [[package]]
 name = "anyio"
-version = "4.4.0"
+version = "4.6.2.post1"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"},
-    {file = "anyio-4.4.0.tar.gz", hash = "sha256:5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94"},
+    {file = "anyio-4.6.2.post1-py3-none-any.whl", hash = "sha256:6d170c36fba3bdd840c73d3868c1e777e33676a69c3a72cf0a0d5d6d8009b61d"},
+    {file = "anyio-4.6.2.post1.tar.gz", hash = "sha256:4c8bc31ccdb51c7f7bd251f51c609e038d63e34219b44aa86e47576389880b4c"},
 ]
 
 [package.dependencies]
@@ -29,9 +29,9 @@ sniffio = ">=1.1"
 typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
-doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
-test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
-trio = ["trio (>=0.23)"]
+doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
+test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21.0b1)"]
+trio = ["trio (>=0.26.1)"]
 
 [[package]]
 name = "appnope"
@@ -46,28 +46,27 @@ files = [
 
 [[package]]
 name = "apscheduler"
-version = "3.10.4"
+version = "3.11.0"
 description = "In-process task scheduler with Cron-like capabilities"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "APScheduler-3.10.4-py3-none-any.whl", hash = "sha256:fb91e8a768632a4756a585f79ec834e0e27aad5860bac7eaa523d9ccefd87661"},
-    {file = "APScheduler-3.10.4.tar.gz", hash = "sha256:e6df071b27d9be898e486bc7940a7be50b4af2e9da7c08f0744a96d4bd4cef4a"},
+    {file = "APScheduler-3.11.0-py3-none-any.whl", hash = "sha256:fc134ca32e50f5eadcc4938e3a4545ab19131435e851abb40b34d63d5141c6da"},
+    {file = "apscheduler-3.11.0.tar.gz", hash = "sha256:4c622d250b0955a65d5d0eb91c33e6d43fd879834bf541e0a18661ae60460133"},
 ]
 
 [package.dependencies]
-pytz = "*"
-six = ">=1.4.0"
-tzlocal = ">=2.0,<3.dev0 || >=4.dev0"
+tzlocal = ">=3.0"
 
 [package.extras]
-doc = ["sphinx", "sphinx-rtd-theme"]
+doc = ["packaging", "sphinx", "sphinx-rtd-theme (>=1.3.0)"]
+etcd = ["etcd3", "protobuf (<=3.21.0)"]
 gevent = ["gevent"]
 mongodb = ["pymongo (>=3.0)"]
 redis = ["redis (>=3.0)"]
 rethinkdb = ["rethinkdb (>=2.4.0)"]
 sqlalchemy = ["sqlalchemy (>=1.4)"]
-testing = ["pytest", "pytest-asyncio", "pytest-cov", "pytest-tornado5"]
+test = ["APScheduler[etcd,mongodb,redis,rethinkdb,sqlalchemy,tornado,zookeeper]", "PySide6", "anyio (>=4.5.2)", "gevent", "pytest", "pytz", "twisted"]
 tornado = ["tornado (>=4.3)"]
 twisted = ["twisted"]
 zookeeper = ["kazoo"]
@@ -150,13 +149,13 @@ test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock
 
 [[package]]
 name = "asteval"
-version = "1.0.4"
+version = "1.0.5"
 description = "Safe, minimalistic evaluator of python expression using ast module"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "asteval-1.0.4-py3-none-any.whl", hash = "sha256:7a88bfd0dd1eabdf20bb4995904df742cecf876f7f9e700f22231abf4e34d50c"},
-    {file = "asteval-1.0.4.tar.gz", hash = "sha256:15e63bd01fce65aded51357f7e1debc6f46100d777c372af11c27c07cb740074"},
+    {file = "asteval-1.0.5-py3-none-any.whl", hash = "sha256:082b95312578affc8a6d982f7d92b7ac5de05634985c87e7eedd3188d31149fa"},
+    {file = "asteval-1.0.5.tar.gz", hash = "sha256:bac3c8dd6d2b789e959cfec9bb296fb8338eec066feae618c462132701fbc665"},
 ]
 
 [package.extras]
@@ -264,21 +263,20 @@ lxml = ["lxml"]
 
 [[package]]
 name = "bleach"
-version = "6.1.0"
+version = "6.2.0"
 description = "An easy safelist-based HTML-sanitizing tool."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "bleach-6.1.0-py3-none-any.whl", hash = "sha256:3225f354cfc436b9789c66c4ee030194bee0568fbf9cbdad3bc8b5c26c5f12b6"},
-    {file = "bleach-6.1.0.tar.gz", hash = "sha256:0a31f1837963c41d46bbf1331b8778e1308ea0791db03cc4e7357b97cf42a8fe"},
+    {file = "bleach-6.2.0-py3-none-any.whl", hash = "sha256:117d9c6097a7c3d22fd578fcd8d35ff1e125df6736f554da4e432fdd63f31e5e"},
+    {file = "bleach-6.2.0.tar.gz", hash = "sha256:123e894118b8a599fd80d3ec1a6d4cc7ce4e5882b1317a7e1ba69b56e95f991f"},
 ]
 
 [package.dependencies]
-six = ">=1.9.0"
 webencodings = "*"
 
 [package.extras]
-css = ["tinycss2 (>=1.1.0,<1.3)"]
+css = ["tinycss2 (>=1.1.0,<1.5)"]
 
 [[package]]
 name = "brukeropusreader"
@@ -386,101 +384,116 @@ pycparser = "*"
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.2"
+version = "3.4.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
 files = [
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 [[package]]
@@ -527,76 +540,65 @@ test = ["pytest"]
 
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 optional = false
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 [package.dependencies]
@@ -611,38 +613,38 @@ test-no-images = ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist"
 
 [[package]]
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 optional = false
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 [package.dependencies]
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 sdist = ["build"]
 ssh = ["bcrypt (>=3.1.5)"]
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 test-randomorder = ["pytest-randomly"]
 
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 [[package]]
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 ]
 
 [package.extras]
@@ -988,36 +1002,41 @@ tornado = ["tornado"]
 
 [[package]]
 name = "h5py"
-version = "3.11.0"
+version = "3.12.1"
 description = "Read and write HDF5 files from Python"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
-numpy = ">=1.17.3"
+numpy = ">=1.19.3"
 
 [[package]]
 name = "h5pyd"
@@ -1029,7 +1048,7 @@ files = []
 develop = false
 
 [package.dependencies]
-numpy = ">=1.17.3,<2.0.0"
+numpy = {version = ">=2.0.0rc1", markers = "python_version >= \"3.9\""}
 packaging = "*"
 pyjwt = "*"
 pytz = "*"
@@ -1044,8 +1063,8 @@ hdf5 = ["h5py"]
 [package.source]
 type = "git"
 url = "https://github.com/HDFGroup/h5pyd.git"
-reference = "HEAD"
-resolved_reference = "41ff1901b310a9bb15e712a9065561e1d4c775c6"
+reference = "8d1c87ea9b6d4b7691b75ef6e372bc0ece141a76"
+resolved_reference = "8d1c87ea9b6d4b7691b75ef6e372bc0ece141a76"
 
 [[package]]
 name = "hdf5plugin"
@@ -1071,13 +1090,13 @@ test = ["blosc2 (>=2.5.1)", "blosc2-grok (>=0.2.2)"]
 
 [[package]]
 name = "httpcore"
-version = "1.0.5"
+version = "1.0.7"
 description = "A minimal low-level HTTP client."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "httpcore-1.0.5-py3-none-any.whl", hash = "sha256:421f18bac248b25d310f3cacd198d55b8e6125c107797b609ff9b7a6ba7991b5"},
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+    {file = "httpcore-1.0.7-py3-none-any.whl", hash = "sha256:a3fff8f43dc260d5bd363d9f9cf1830fa3a458b332856f34282de498ed420edd"},
+    {file = "httpcore-1.0.7.tar.gz", hash = "sha256:8551cb62a169ec7162ac7be8d4817d561f60e08eaa485234898414bb5a8a0b4c"},
 ]
 
 [package.dependencies]
@@ -1088,7 +1107,7 @@ h11 = ">=0.13,<0.15"
 asyncio = ["anyio (>=4.0,<5.0)"]
 http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
-trio = ["trio (>=0.22.0,<0.26.0)"]
+trio = ["trio (>=0.22.0,<1.0)"]
 
 [[package]]
 name = "httpx"
@@ -1117,13 +1136,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "idna"
-version = "3.9"
+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.6"
 files = [
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+    {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"},
+    {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"},
 ]
 
 [package.extras]
@@ -1175,13 +1194,13 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio
 
 [[package]]
 name = "ipython"
-version = "8.27.0"
+version = "8.29.0"
 description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.10"
 files = [
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+    {file = "ipython-8.29.0.tar.gz", hash = "sha256:40b60e15b22591450eef73e40a027cf77bd652e757523eebc5bd7c7c498290eb"},
 ]
 
 [package.dependencies]
@@ -1248,22 +1267,22 @@ arrow = ">=0.15.0"
 
 [[package]]
 name = "jedi"
-version = "0.19.1"
+version = "0.19.2"
 description = "An autocompletion tool for Python that can be used for text editors."
 optional = false
 python-versions = ">=3.6"
 files = [
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-    {file = "jedi-0.19.1.tar.gz", hash = "sha256:cf0496f3651bc65d7174ac1b7d043eff454892c708a87d1b683e57b569927ffd"},
+    {file = "jedi-0.19.2-py2.py3-none-any.whl", hash = "sha256:a8ef22bde8490f57fe5c7681a3c83cb58874daf72b4784de3cce5b6ef6edb5b9"},
+    {file = "jedi-0.19.2.tar.gz", hash = "sha256:4770dc3de41bde3966b02eb84fbcf557fb33cce26ad23da12c742fb50ecb11f0"},
 ]
 
 [package.dependencies]
-parso = ">=0.8.3,<0.9.0"
+parso = ">=0.8.4,<0.9.0"
 
 [package.extras]
 docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"]
 qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
-testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
+testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"]
 
 [[package]]
 name = "jinja2"
@@ -1309,15 +1328,18 @@ six = ">=1.13,<2.0"
 
 [[package]]
 name = "json5"
-version = "0.9.25"
+version = "0.9.28"
 description = "A Python implementation of the JSON5 data format."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.8.0"
 files = [
-    {file = "json5-0.9.25-py3-none-any.whl", hash = "sha256:34ed7d834b1341a86987ed52f3f76cd8ee184394906b6e22a1e0deb9ab294e8f"},
-    {file = "json5-0.9.25.tar.gz", hash = "sha256:548e41b9be043f9426776f05df8635a00fe06104ea51ed24b67f908856e151ae"},
+    {file = "json5-0.9.28-py3-none-any.whl", hash = "sha256:29c56f1accdd8bc2e037321237662034a7e07921e2b7223281a5ce2c46f0c4df"},
+    {file = "json5-0.9.28.tar.gz", hash = "sha256:1f82f36e615bc5b42f1bbd49dbc94b12563c56408c6ffa06414ea310890e9a6e"},
 ]
 
+[package.extras]
+dev = ["build (==1.2.2.post1)", "coverage (==7.5.3)", "mypy (==1.13.0)", "pip (==24.3.1)", "pylint (==3.2.3)", "ruff (==0.7.3)", "twine (==5.1.1)", "uv (==0.5.1)"]
+
 [[package]]
 name = "jsonpointer"
 version = "3.0.0"
@@ -1360,13 +1382,13 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2023.12.1"
+version = "2024.10.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 [package.dependencies]
@@ -1393,13 +1415,13 @@ notebook = "*"
 
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+version = "8.6.3"
 description = "Jupyter protocol implementation and client libraries"
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@@ -1553,13 +1575,13 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>
 
 [[package]]
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 traitlets = "*"
 
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 [[package]]
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 python-versions = ">=3.6"
 files = [
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 [package.dependencies]
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 [package.extras]
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 ]
 
 [package.dependencies]
@@ -2463,18 +2526,17 @@ testing = ["docopt", "pytest"]
 
 [[package]]
 name = "patsy"
-version = "0.5.6"
+version = "1.0.1"
 description = "A Python package for describing statistical models and for building design matrices."
 optional = false
-python-versions = "*"
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 ]
 
 [package.dependencies]
 numpy = ">=1.4"
-six = "*"
 
 [package.extras]
 test = ["pytest", "pytest-cov", "scipy"]
@@ -2495,95 +2557,90 @@ ptyprocess = ">=0.5"
 
 [[package]]
 name = "pillow"
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 description = "Python Imaging Library (Fork)"
 optional = false
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 [package.extras]
-docs = ["furo", "olefile", "sphinx (>=7.3)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"]
+docs = ["furo", "olefile", "sphinx (>=8.1)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"]
 fpx = ["olefile"]
 mic = ["olefile"]
 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
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 [[package]]
 name = "platformdirs"
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 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
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 [[package]]
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 [package.extras]
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 [[package]]
 name = "prompt-toolkit"
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+version = "3.0.48"
 description = "Library for building powerful interactive command lines in Python"
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 [package.dependencies]
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 [package.extras]
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+test = ["pytest", "pytest-xdist", "setuptools"]
 
 [[package]]
 name = "ptyprocess"
@@ -2708,20 +2766,16 @@ name = "pyambit"
 version = "0.0.1"
 description = "Python implementation of AMBIT data model"
 optional = false
-python-versions = ">=3.9,<4.0"
-files = []
-develop = false
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 [package.dependencies]
@@ -2857,13 +2922,13 @@ typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
 
 [[package]]
 name = "pydantic-settings"
-version = "2.5.2"
+version = "2.6.1"
 description = "Settings management using Pydantic"
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 python-versions = ">=3.8"
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@@ -2891,13 +2956,13 @@ windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
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-version = "2.9.0"
+version = "2.10.0"
 description = "JSON Web Token implementation in Python"
 optional = false
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 [[package]]
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 description = "eNanoMapper API client"
 optional = false
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-files = []
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-type = "directory"
-url = "extern/pynanomapper"
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 [package.extras]
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 version = "1.2.0"
 description = "Harmonising Raman Spectroscopy"
 optional = false
-python-versions = ">=3.9,<3.13"
-files = []
-develop = true
+python-versions = "<3.13,>=3.9"
+files = [
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 [package.dependencies]
 brukeropusreader = "==1.*"
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 scikit-learn = "==1.*"
 scipy = ">=1.8.0,<2.0"
 spc-io = ">=0.2.0,<0.3.0"
-spe2py = ">=2.0,<3.0"
 statsmodels = "==0.14.*"
 uncertainties = "==3.*"
 
-[package.source]
-type = "directory"
-url = "extern/ramanchada2"
-
 [[package]]
 name = "referencing"
 version = "0.35.1"
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 pandas = "*"
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 [package.dependencies]
-numpy = ">=1.22.3"
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 packaging = ">=21.3"
 pandas = ">=1.4,<2.1.0 || >2.1.0"
 patsy = ">=0.5.6"
 scipy = ">=1.8,<1.9.2 || >1.9.2"
 
 [package.extras]
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+build = ["cython (>=3.0.10)"]
+develop = ["colorama", "cython (>=3.0.10)", "cython (>=3.0.10,<4)", "flake8", "isort", "joblib", "matplotlib (>=3)", "pytest (>=7.3.0,<8)", "pytest-cov", "pytest-randomly", "pytest-xdist", "pywinpty", "setuptools-scm[toml] (>=8.0,<9.0)"]
 docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"]
 
 [[package]]
 name = "sympy"
-version = "1.13.2"
+version = "1.13.3"
 description = "Computer algebra system (CAS) in Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -3888,13 +3924,13 @@ files = [
 
 [[package]]
 name = "tifffile"
-version = "2024.8.30"
+version = "2024.9.20"
 description = "Read and write TIFF files"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 files = [
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 ]
 
 [package.dependencies]
@@ -3910,13 +3946,13 @@ zarr = ["fsspec", "zarr"]
 
 [[package]]
 name = "tinycss2"
-version = "1.3.0"
+version = "1.4.0"
 description = "A tiny CSS parser"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -3928,33 +3964,33 @@ test = ["pytest", "ruff"]
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.1.0"
 description = "A lil' TOML parser"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "tornado"
-version = "6.4.1"
+version = "6.4.2"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -3974,13 +4010,13 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,
 
 [[package]]
 name = "types-python-dateutil"
-version = "2.9.0.20240906"
+version = "2.9.0.20241003"
 description = "Typing stubs for python-dateutil"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -3996,13 +4032,13 @@ files = [
 
 [[package]]
 name = "tzdata"
-version = "2024.1"
+version = "2024.2"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 files = [
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 ]
 
 [[package]]
@@ -4039,20 +4075,6 @@ arrays = ["numpy"]
 doc = ["python-docs-theme", "sphinx", "sphinx-copybutton"]
 test = ["pytest", "pytest-cov"]
 
-[[package]]
-name = "untangle"
-version = "1.2.1"
-description = "Converts XML to Python objects"
-optional = false
-python-versions = ">=3.7,<4.0"
-files = [
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-
-[package.dependencies]
-defusedxml = ">=0.7.1,<0.8.0"
-
 [[package]]
 name = "uri-template"
 version = "1.3.0"
@@ -4116,19 +4138,15 @@ files = [
 
 [[package]]
 name = "webcolors"
-version = "24.8.0"
+version = "24.11.1"
 description = "A library for working with the color formats defined by HTML and CSS."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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-    {file = "webcolors-24.8.0.tar.gz", hash = "sha256:08b07af286a01bcd30d583a7acadf629583d1f79bfef27dd2c2c5c263817277d"},
+    {file = "webcolors-24.11.1-py3-none-any.whl", hash = "sha256:515291393b4cdf0eb19c155749a096f779f7d909f7cceea072791cb9095b92e9"},
+    {file = "webcolors-24.11.1.tar.gz", hash = "sha256:ecb3d768f32202af770477b8b65f318fa4f566c22948673a977b00d589dd80f6"},
 ]
 
-[package.extras]
-docs = ["furo", "sphinx", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-notfound-page", "sphinxext-opengraph"]
-tests = ["coverage[toml]"]
-
 [[package]]
 name = "webencodings"
 version = "0.5.1"
@@ -4181,4 +4199,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.10,<3.13"
-content-hash = "f565af1f10230400c4755b6ebf125e1226ebc1c1b472164507fe06cc05da1cd7"
+content-hash = "cbd93bef1ea2bd0a4ee16a103bc7fb7a22c7b2f00fac61aec65d97e79c1252e2"
diff --git a/pyproject.toml b/pyproject.toml
index c9cfe08..178f8af 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,14 +24,15 @@ python = ">=3.10,<3.13"
 apscheduler = "^3.10.1"
 fastapi = "^0.112.1"
 h5grove = "^2.0.0"
-h5pyd = { git = "https://github.com/HDFGroup/h5pyd.git" }
+h5pyd = { git = "https://github.com/HDFGroup/h5pyd.git", rev = "8d1c87ea9b6d4b7691b75ef6e372bc0ece141a76" }
 numcompress = "^0.1.2"
 openpyxl = "^3.1.2"
+pyambit = "^0.0.1"
 pydantic-settings = "^2.4.0"
-pynanomapper = { path = "extern/pynanomapper", develop = true }
+pynanomapper = "^2.0.1"
 python-keycloak = "^4.3.0"
 python-multipart = "^0.0.6"
-ramanchada2 = { path = "extern/ramanchada2", develop = true }
+ramanchada2 = "^1.2.0"
 uvicorn = "^0.27.1"
 
 [tool.poetry.urls]

From b4989b750119e37bc52b9e8510dd76ffab3d1a52 Mon Sep 17 00:00:00 2001
From: Luchesar ILIEV <luchesar.iliev@gmail.com>
Date: Tue, 26 Nov 2024 15:23:44 +0200
Subject: [PATCH 2/6] remove now unnecessary submodules

---
 .gitmodules         | 6 ------
 extern/pynanomapper | 1 -
 extern/ramanchada2  | 1 -
 3 files changed, 8 deletions(-)
 delete mode 160000 extern/pynanomapper
 delete mode 160000 extern/ramanchada2

diff --git a/.gitmodules b/.gitmodules
index b698f2f..e69de29 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,6 +0,0 @@
-[submodule "pynanomapper"]
-	path = extern/pynanomapper
-	url = https://github.com/ideaconsult/pynanomapper.git
-[submodule "ramanchada2"]
-	path = extern/ramanchada2
-	url = https://github.com/h2020charisma/ramanchada2.git
diff --git a/extern/pynanomapper b/extern/pynanomapper
deleted file mode 160000
index f9e9e3d..0000000
--- a/extern/pynanomapper
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit f9e9e3d3437c210f2b944ff05ce00e22882721cf
diff --git a/extern/ramanchada2 b/extern/ramanchada2
deleted file mode 160000
index d7b4e2b..0000000
--- a/extern/ramanchada2
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit d7b4e2bdc9262a84833fa4ebc9ef39b6feb34aa6

From f9ee2dec7bd50ad52a99fc2539c0fa335e1b4405 Mon Sep 17 00:00:00 2001
From: Luchesar ILIEV <luchesar.iliev@gmail.com>
Date: Tue, 26 Nov 2024 15:28:13 +0200
Subject: [PATCH 3/6] docker: update for new dependency setup

---
 Dockerfile | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index e578be8..5ba8be2 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,12 +2,9 @@ FROM python:3.11-slim AS requirements-stage
 
 WORKDIR /tmp
 
-RUN pip install poetry
-
 COPY ./pyproject.toml ./poetry.lock* /tmp/
-COPY ./extern/pynanomapper /tmp/extern/pynanomapper
-COPY ./extern/ramanchada2 /tmp/extern/ramanchada2
 
+RUN pip install poetry
 RUN poetry export -f requirements.txt --output requirements.txt --without=dev --without-hashes
 
 
@@ -18,14 +15,6 @@ RUN apt-get update && apt-get install -y \
     && rm -rf /var/lib/apt/lists/*
 
 COPY --from=requirements-stage /tmp/requirements.txt /app/requirements.txt
-COPY ./extern/pynanomapper /tmp/extern/pynanomapper
-COPY ./extern/ramanchada2 /tmp/extern/ramanchada2
-
-RUN sed -i 's/^-e //' /app/requirements.txt
-
-# FIXME: 809de9f workaround introduced discrepancy between poetry.lock and this installation.
-# This is another "fix" that'll come back to bite us until we fix the whole dependency thing.
-RUN sed -i '/^pyambit/d' /tmp/extern/pynanomapper/pyproject.toml
 
 RUN pip install --no-cache-dir --upgrade -r /app/requirements.txt
 

From 4fd3fe31d9db41be2322ed94171c836a34b95166 Mon Sep 17 00:00:00 2001
From: Luchesar ILIEV <luchesar.iliev@gmail.com>
Date: Tue, 26 Nov 2024 15:30:10 +0200
Subject: [PATCH 4/6] ops: update dependabot config

---
 .github/dependabot.yml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index 55cca57..32a9e3c 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -6,7 +6,16 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "monthly"
+      interval: "weekly"
+    target-branch: "develop"
+    assignees:
+      - "kerberizer"
+
+  # Maintain dependencies for Python
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
     target-branch: "develop"
     assignees:
       - "kerberizer"

From 78fa7dcc83c82874a24aea3622c016c1e2b55630 Mon Sep 17 00:00:00 2001
From: Luchesar ILIEV <luchesar.iliev@gmail.com>
Date: Tue, 26 Nov 2024 15:32:15 +0200
Subject: [PATCH 5/6] ops: update poetry and cosign versions

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 928104f..2527b0e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -17,7 +17,7 @@ on:  # yamllint disable-line rule:truthy
   workflow_dispatch:
 
 env:
-  POETRY_VERSION: 1.8.3
+  POETRY_VERSION: 1.8.4
   REGISTRY: ghcr.io
   IMAGE_NAME: ${{ github.repository }}
 
@@ -113,7 +113,7 @@ jobs:
         if: github.event_name != 'pull_request'
         uses: sigstore/cosign-installer@v3.6.0
         with:
-          cosign-release: 'v2.4.0'
+          cosign-release: 'v2.4.1'
 
       # Workaround: https://github.com/docker/build-push-action/issues/461
       - name: Setup Docker buildx

From 8cb0c5dac90d371a407301b9a36edc93974a9608 Mon Sep 17 00:00:00 2001
From: vedina <jeliazkova.nina@gmail.com>
Date: Tue, 26 Nov 2024 16:48:02 +0200
Subject: [PATCH 6/6] this was an old attempt to provide API for calibration
 not used at the moment removed

---
 src/rcapi/services/process_service.py    | 46 ++++++------------------
 src/rcapi/services/processing_spectra.py | 37 ++++---------------
 2 files changed, 17 insertions(+), 66 deletions(-)

diff --git a/src/rcapi/services/process_service.py b/src/rcapi/services/process_service.py
index 80803c4..95dc6dc 100644
--- a/src/rcapi/services/process_service.py
+++ b/src/rcapi/services/process_service.py
@@ -1,45 +1,21 @@
 import os
-import uuid
 import time
-import shutil
 from rcapi.models.models import Task  # Import your data models
-import h5py
 from ..config.app_config import load_config
-from pyambit.nexus_parser import SpectrumParser
 
-config = load_config()
-async def process(task : Task,process_config : dict, nexus_dataset_url: str,base_url: str):
-    try:
-        process_class = process_config["class"]
-        process_class.process(task,nexus_dataset_url,base_url)
 
-        task.status = "Completed"
-    except (ImportError, AttributeError) as e:
-        task.status = "Error"
-        task.error = f"Failed to load plugin or class: {e}"
-    except Exception as e:
-        task.status = "Error"
-        task.error = f"{e}"   
-    task.completed=int(time.time() * 1000)  
+config = load_config()
 UPLOAD_DIR = config.upload_dir
 os.makedirs(UPLOAD_DIR, exist_ok=True)
 
-async def process_new(task : Task,nexus_dataset_url: str,base_url: str):
-    open_dataset(nexus_dataset_url,base_url)
-    task.status = "Completed"
-    task.completed=int(time.time() * 1000)
-    
 
-def open_dataset(nexus_dataset_url: str,base_url: str):
-    if nexus_dataset_url.startswith(base_url):
-        uuid = nexus_dataset_url.split("/")[-1]
-        spectrum_parser = SpectrumParser()
-        spectrum_parser.parse(os.path.join(UPLOAD_DIR,f"{uuid}.nxs"))
-        # Access the spectrum data
-        for key in spectrum_parser.parsed_objects:
-            spe = spectrum_parser.parsed_objects[key]
-            print("Spectrum data", key, spe)
-            #spe.plot()     
-        
-    else:
-        pass
\ No newline at end of file
+async def process(task: Task, process_config: dict,
+                  nexus_dataset_url: str, base_url: str):
+    task.status = "Error"
+    task.error = "Not implemented"
+    task.completed = int(time.time() * 1000)
+
+
+async def process_new(task: Task, nexus_dataset_url: str, base_url: str):
+    task.status = "Error"
+    task.completed = int(time.time() * 1000)
diff --git a/src/rcapi/services/processing_spectra.py b/src/rcapi/services/processing_spectra.py
index cef80fe..e064e36 100644
--- a/src/rcapi/services/processing_spectra.py
+++ b/src/rcapi/services/processing_spectra.py
@@ -1,45 +1,20 @@
-import os
 from rcapi.config.app_config import initialize_dirs
 from rcapi.models.models import Task
-from pyambit.nexus_parser import SpectrumParser
-from pyambit.nexus_spectra import peaks2nxdata
 
-#from ramanchada2.protocols.calibration import CalibrationModel
 
 config, UPLOAD_DIR, NEXUS_DIR, TEMPLATE_DIR = initialize_dirs()
 
-def open_dataset(nexus_dataset_url: str,base_url: str):
-    print(nexus_dataset_url,base_url)
-    if nexus_dataset_url.startswith(base_url):
-        uuid = nexus_dataset_url.split("/")[-1]
-        spectrum_parser = SpectrumParser()
-        spectrum_parser.parse(os.path.join(NEXUS_DIR,f"{uuid}.nxs"))
-        return spectrum_parser
-    else:
-        return None
 
 class ProcessMock:
-    def process(task : Task,nexus_dataset_url: str,base_url: str):
-        spectrum_parser : SpectrumParser = open_dataset(nexus_dataset_url,base_url)
-        for key in spectrum_parser.parsed_objects:
-            spe = spectrum_parser.parsed_objects[key]
-            print("Spectrum data", key, spe)
-            #spe.plot()     
+    def process(task: Task, nexus_dataset_url: str, base_url: str):
+        pass
 
 
 class ProcessCalibrate:
-    def process(task : Task,nexus_dataset_url: str,base_url: str):
-        #calmodel = CalibrationModel(laser_wl)
-        #calmodel.derive_model_x(spe_neon,spe_neon_units="cm-1",ref_neon=None,ref_neon_units="nm",spe_sil=None,spe_sil_units="cm-1",ref_sil=None,ref_sil_units="cm-1")
+    def process(task: Task, nexus_dataset_url: str, base_url: str):
         pass
-       
+
 
 class ProcessFindPeak:
-    def process(task : Task,nexus_dataset_url: str,base_url: str):
-        spectrum_parser : SpectrumParser = open_dataset(nexus_dataset_url,base_url)
-        for key in spectrum_parser.parsed_objects:
-            spe = spectrum_parser.parsed_objects[key]
-            print("Spectrum data", key, spe)
-            peak_candidates = spe.find_peak_multipeak(sharpening='hht', strategy='topo')
-            fitres = spe.fit_peak_multimodel(profile='Moffat', candidates=peak_candidates, no_fit=True)
-            print(fitres.to_dataframe_peaks())
+    def process(task: Task, nexus_dataset_url: str, base_url: str):
+        pass