diff --git a/conda-lock.yml b/conda-lock.yml index 0addb4e..944fe92 100644 --- a/conda-lock.yml +++ b/conda-lock.yml @@ -2877,39 +2877,39 @@ package: category: main optional: false - name: pycparser - version: '2.21' + version: '2.22' manager: conda platform: linux-64 dependencies: - python: 2.7.*|>=3.4 - url: https://conda.anaconda.org/conda-forge/noarch/pycparser-2.21-pyhd8ed1ab_0.tar.bz2 + python: '>=3.8' + url: https://conda.anaconda.org/conda-forge/noarch/pycparser-2.22-pyhd8ed1ab_0.conda hash: - md5: 076becd9e05608f8dc72757d5f3a91ff - sha256: 74c63fd03f1f1ea2b54e8bc529fd1a600aaafb24027b738d0db87909ee3a33dc + md5: 844d9eb3b43095b031874477f7d70088 + sha256: 406001ebf017688b1a1554b49127ca3a4ac4626ec0fd51dc75ffa4415b720b64 category: main optional: false - name: pycparser - version: '2.21' + version: '2.22' manager: conda platform: osx-64 dependencies: - python: 2.7.*|>=3.4 - url: https://conda.anaconda.org/conda-forge/noarch/pycparser-2.21-pyhd8ed1ab_0.tar.bz2 + python: '>=3.8' + url: https://conda.anaconda.org/conda-forge/noarch/pycparser-2.22-pyhd8ed1ab_0.conda hash: - md5: 076becd9e05608f8dc72757d5f3a91ff - sha256: 74c63fd03f1f1ea2b54e8bc529fd1a600aaafb24027b738d0db87909ee3a33dc + md5: 844d9eb3b43095b031874477f7d70088 + sha256: 406001ebf017688b1a1554b49127ca3a4ac4626ec0fd51dc75ffa4415b720b64 category: main optional: false - name: pycparser - version: '2.21' + version: '2.22' manager: conda platform: win-64 dependencies: - python: 2.7.*|>=3.4 - url: https://conda.anaconda.org/conda-forge/noarch/pycparser-2.21-pyhd8ed1ab_0.tar.bz2 + python: '>=3.8' + url: https://conda.anaconda.org/conda-forge/noarch/pycparser-2.22-pyhd8ed1ab_0.conda hash: - md5: 076becd9e05608f8dc72757d5f3a91ff - sha256: 74c63fd03f1f1ea2b54e8bc529fd1a600aaafb24027b738d0db87909ee3a33dc + md5: 844d9eb3b43095b031874477f7d70088 + sha256: 406001ebf017688b1a1554b49127ca3a4ac4626ec0fd51dc75ffa4415b720b64 category: main optional: false - name: pydantic diff --git a/environment.yml b/environment.yml index 09b1e8c..fb8e705 100644 --- a/environment.yml +++ b/environment.yml @@ -1,5 +1,6 @@ name: subpex-dev channels: + - conda-forge - defaults dependencies: - python=3.12 diff --git a/poetry.lock b/poetry.lock index 5c999d7..7d660a0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2447,13 +2447,13 @@ files = [ [[package]] name = "pycparser" -version = "2.21" +version = "2.22" description = "C parser in Python" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.8" files = [ - {file = "pycparser-2.21-py2.py3-none-any.whl", hash = "sha256:8ee45429555515e1f6b185e78100aea234072576aa43ab53aefcae078162fca9"}, - {file = "pycparser-2.21.tar.gz", hash = "sha256:e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206"}, + {file = "pycparser-2.22-py3-none-any.whl", hash = "sha256:c3702b6d3dd8c7abc1afa565d7e63d53a1d0bd86cdc24edd75470f4de499cfcc"}, + {file = "pycparser-2.22.tar.gz", hash = "sha256:491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6"}, ] [[package]] diff --git a/pyproject.toml b/pyproject.toml index c69260f..39dcf21 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -182,81 +182,84 @@ show_missing = true ["tool.poetry.group.conda.dependencies"] appdirs = "^1.4.4" -Brotli = "^1.0.9" +Brotli = "^1.1.0" build = "^1.2.1" CacheControl = "^0.14.0" cachy = "^0.3.0" certifi = "^2024.2.2" cffi = "^1.16.0" cfgv = "^3.3.1" -charset-normalizer = "^2.0.4" +charset-normalizer = "^3.3.2" cleo = "^2.1.0" click = "^8.1.7" -click-default-group = "^1.2.2" +click-default-group = "^1.2.4" clikit = "^0.6.2" colorama = "^0.4.6" conda_lock = "^2.5.6" conda_poetry_liaison = "^0.1.2" crashtest = "^0.4.1" cryptography = "^42.0.5" -distlib = "^0.3.6" -dulwich = "^0.21.3" +distlib = "^0.3.8" +dulwich = "^0.21.7" ensureconda = "^1.4.4" fastjsonschema = "^2.19.1" -filelock = "^3.13.1" -gitdb = "^4.0.7" -GitPython = "^3.1.37" +filelock = "^3.13.3" +gitdb = "^4.0.11" +GitPython = "^3.1.42" html5lib = "^1.1" identify = "^2.5.35" -idna = "^3.4" +idna = "^3.6" importlib_metadata = "^7.1.0" +importlib_resources = "^6.4.0" installer = "^0.7.0" -"jaraco.classes" = "^3.2.1" -jeepney = "^0.7.1" +"jaraco.classes" = "^3.3.1" +"jaraco.context" = "^4.3.0" +"jaraco.functools" = "^4.0.0" +jeepney = "^0.8.0" Jinja2 = "^3.1.3" keyring = "^24.3.1" -MarkupSafe = "^2.1.3" -more-itertools = "^10.1.0" -msgpack = "^1.0.3" +MarkupSafe = "^2.1.5" +more-itertools = "^10.2.0" +msgpack = "^1.0.7" nodeenv = "^1.8.0" numpy = "^1.26.4" -packaging = "^23.2" +packaging = "^24.0" pastel = "^0.2.1" pexpect = "^4.9.0" -pip = "^23.3.1" -pkginfo = "^1.9.6" -platformdirs = "^3.11.0" +pip = "^24.0" +pkginfo = "^1.10.0" +platformdirs = "^4.2.0" poetry = "^1.8.2" poetry-core = "^1.9.0" poetry-plugin-export = "^1.7.1" pre_commit = "^3.7.0" ptyprocess = "^0.7.0" -pycparser = "^2.21" -pydantic = "^2.5.3" -pydantic_core = "^2.14.6" -pylev = "^1.3.0" -pyOpenSSL = "^24.0.0" +pycparser = "^2.22" +pydantic = "^2.6.4" +pydantic_core = "^2.16.3" +pylev = "^1.4.0" pyproject_hooks = "^1.0.0" PySocks = "^1.7.1" PyYAML = "^6.0.1" -rapidfuzz = "^3.5.2" +rapidfuzz = "^3.7.0" requests = "^2.31.0" requests-toolbelt = "^1.0.0" -"ruamel.yaml" = "^0.17.21" -SecretStorage = "^3.3.1" -setuptools = "^68.2.2" +"ruamel.yaml" = "^0.18.6" +"ruamel.yaml.clib" = "^0.2.8" +SecretStorage = "^3.3.3" +setuptools = "^69.2.0" shellingham = "^1.5.4" six = "^1.16.0" -smmap = "^4.0.0" +smmap = "^5.0.0" tomli = "^2.0.1" tomli_w = "^1.0.0" tomlkit = "^0.12.4" -toolz = "^0.12.0" +toolz = "^0.12.1" trove-classifiers = "^2024.3.25" -typing_extensions = "^4.9.0" +typing_extensions = "^4.10.0" ukkonen = "^1.0.1" urllib3 = "^1.26.18" -virtualenv = "^20.24.1" +virtualenv = "^20.25.1" webencodings = "^0.5.1" -wheel = "^0.41.2" +wheel = "^0.43.0" zipp = "^3.17.0" diff --git a/subpex/utils/vis_progress.py b/subpex/utils/vis_progress.py index bc568c7..6a5c05e 100644 --- a/subpex/utils/vis_progress.py +++ b/subpex/utils/vis_progress.py @@ -15,8 +15,8 @@ def rolling_average(data: List[float], window: int) -> List[float]: smaller. Args: - data (list): list of the data to obtain the rolling average. - window (int): size of the window to use. + data: list of the data to obtain the rolling average. + window: size of the window to use. Returns: average (list): list containing the rolling average. @@ -348,7 +348,7 @@ def obtain_paths_highest_rmsd_jd_weight( parser.add_argument( "outdir", type=str, - help="Define the output directory to put the files in, it will creat it if it does not exist. It is required", + help="Define the output directory to put the files in, it will create it if it does not exist. It is required", ) args = parser.parse_args()