diff --git a/mersearch/vendors/vwr.py b/mersearch/vendors/vwr.py index 6b0e0bb..abf40e7 100644 --- a/mersearch/vendors/vwr.py +++ b/mersearch/vendors/vwr.py @@ -339,7 +339,7 @@ def extract_mol_data( elif len(td) == 5: try: row["amount"] = td[2].text.strip() - row["unit"] = td[3].text.strip() + row["units"] = td[3].text.strip() row["price"] = td[4].text.strip() price_data.append(row.copy()) except Exception as e: diff --git a/poetry.lock b/poetry.lock index ec612b3..682c7ec 100644 --- a/poetry.lock +++ b/poetry.lock @@ -80,7 +80,7 @@ six = "*" test = ["astroid", "pytest"] [[package]] -name = "async-generator" +name = "async_generator" version = "1.10" description = "Async generators and context managers for Python 3.5+" category = "main" @@ -100,7 +100,8 @@ cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"] dev = ["attrs[docs,tests]"] docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"] tests = ["attrs[tests-no-zope]", "zope.interface"] -tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"] +tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=0.971,<0.990)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +tests_no_zope = ["cloudpickle", "hypothesis", "mypy (>=0.971,<0.990)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] [[package]] name = "backcall" @@ -112,7 +113,7 @@ python-versions = "*" [[package]] name = "beautifulsoup4" -version = "4.11.2" +version = "4.12.0" description = "Screen-scraping library" category = "main" optional = false @@ -127,7 +128,7 @@ lxml = ["lxml"] [[package]] name = "black" -version = "23.1.0" +version = "23.3.0" description = "The uncompromising code formatter." category = "dev" optional = false @@ -183,11 +184,11 @@ pycparser = "*" [[package]] name = "charset-normalizer" -version = "3.0.1" +version = "3.1.0" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "main" optional = false -python-versions = "*" +python-versions = ">=3.7.0" [[package]] name = "click" @@ -210,7 +211,7 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7 [[package]] name = "comm" -version = "0.1.2" +version = "0.1.3" description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc." category = "dev" optional = false @@ -220,7 +221,9 @@ python-versions = ">=3.6" traitlets = ">=5.3" [package.extras] +lint = ["black (>=22.6.0)", "mdformat (>0.7)", "mdformat-gfm (>=0.3.5)", "ruff (>=0.0.156)"] test = ["pytest"] +typing = ["mypy (>=0.990)"] [[package]] name = "debugpy" @@ -248,7 +251,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "exceptiongroup" -version = "1.1.0" +version = "1.1.1" description = "Backport of PEP 654 (exception groups)" category = "main" optional = false @@ -313,7 +316,7 @@ python-versions = ">=3.7" [[package]] name = "ipykernel" -version = "6.21.2" +version = "6.22.0" description = "IPython Kernel for Jupyter" category = "dev" optional = false @@ -343,7 +346,7 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio" [[package]] name = "ipython" -version = "8.11.0" +version = "8.12.0" description = "IPython: Productive Interactive Computing" category = "dev" optional = false @@ -374,10 +377,10 @@ notebook = ["ipywidgets", "notebook"] parallel = ["ipyparallel"] qtconsole = ["qtconsole"] test = ["pytest (<7.1)", "pytest-asyncio", "testpath"] -test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"] +test_extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"] [[package]] -name = "ipython-genutils" +name = "ipython_genutils" version = "0.2.0" description = "Vestigial utilities from IPython" category = "dev" @@ -412,7 +415,7 @@ qa = ["flake8 (==3.8.3)", "mypy (==0.782)"] testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] [[package]] -name = "jinja2" +name = "Jinja2" version = "3.1.2" description = "A very fast and expressive template engine." category = "dev" @@ -459,7 +462,7 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- [[package]] name = "jupyter-client" -version = "8.0.3" +version = "8.1.0" description = "Jupyter protocol implementation and client libraries" category = "dev" optional = false @@ -478,7 +481,7 @@ test = ["codecov", "coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-co [[package]] name = "jupyter-core" -version = "5.2.0" +version = "5.3.0" description = "Jupyter core package. A base package on which Jupyter projects rely." category = "dev" optional = false @@ -486,7 +489,7 @@ python-versions = ">=3.8" [package.dependencies] platformdirs = ">=2.5" -pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""} +pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""} traitlets = ">=5.3" [package.extras] @@ -516,7 +519,7 @@ test = ["click", "coverage", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>= [[package]] name = "jupyter-server" -version = "2.3.0" +version = "2.5.0" description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications." category = "dev" optional = false @@ -543,7 +546,7 @@ traitlets = ">=5.6.0" websocket-client = "*" [package.extras] -docs = ["docutils (<0.20)", "ipykernel", "jinja2", "jupyter-client", "jupyter-server", "mistune (<1.0.0)", "myst-parser", "nbformat", "prometheus-client", "pydata-sphinx-theme", "send2trash", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-openapi", "sphinxcontrib-spelling", "sphinxemoji", "tornado"] +docs = ["docutils (<0.20)", "ipykernel", "jinja2", "jupyter-client", "jupyter-server", "mistune (<1.0.0)", "myst-parser", "nbformat", "prometheus-client", "pydata-sphinx-theme", "send2trash", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-openapi", "sphinxcontrib-spelling", "sphinxemoji", "tornado", "typing-extensions"] test = ["ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-scripts", "pytest-jupyter[server] (>=0.4)", "pytest-timeout", "requests"] [[package]] @@ -585,7 +588,7 @@ htmlsoup = ["BeautifulSoup4"] source = ["Cython (>=0.29.7)"] [[package]] -name = "markupsafe" +name = "MarkupSafe" version = "2.1.2" description = "Safely add untrusted strings to HTML/XML markup." category = "dev" @@ -621,7 +624,7 @@ python-versions = ">=3.5" [[package]] name = "nbclassic" -version = "0.5.2" +version = "0.5.4" description = "Jupyter Notebook as a Jupyter Server extension." category = "dev" optional = false @@ -672,7 +675,7 @@ test = ["ipykernel", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>= [[package]] name = "nbconvert" -version = "7.2.9" +version = "7.2.10" description = "Converting Jupyter Notebooks" category = "dev" optional = false @@ -706,7 +709,7 @@ webpdf = ["pyppeteer (>=1,<1.1)"] [[package]] name = "nbformat" -version = "5.7.3" +version = "5.8.0" description = "The Jupyter Notebook format" category = "dev" optional = false @@ -732,7 +735,7 @@ python-versions = ">=3.5" [[package]] name = "notebook" -version = "6.5.2" +version = "6.5.3" description = "A web-based notebook environment for interactive computing" category = "dev" optional = false @@ -843,7 +846,7 @@ testing = ["docopt", "pytest (<6.0.0)"] [[package]] name = "pathspec" -version = "0.11.0" +version = "0.11.1" description = "Utility library for gitignore style pattern matching of file paths." category = "dev" optional = false @@ -869,7 +872,7 @@ optional = false python-versions = "*" [[package]] -name = "pillow" +name = "Pillow" version = "9.4.0" description = "Python Imaging Library (Fork)" category = "main" @@ -882,7 +885,7 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa [[package]] name = "platformdirs" -version = "3.0.0" +version = "3.2.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." category = "dev" optional = false @@ -890,7 +893,7 @@ python-versions = ">=3.7" [package.extras] docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"] -test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"] +test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"] [[package]] name = "pluggy" @@ -965,7 +968,7 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] -name = "pygments" +name = "Pygments" version = "2.14.0" description = "Pygments is a syntax highlighting package written in Python." category = "dev" @@ -984,7 +987,7 @@ optional = false python-versions = ">=3.7" [[package]] -name = "pysocks" +name = "PySocks" version = "1.7.1" description = "A Python SOCKS client module. See https://github.com/Anorov/PySocks for more information." category = "main" @@ -993,7 +996,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pytest" -version = "7.2.1" +version = "7.2.2" description = "pytest: simple powerful testing with Python" category = "dev" optional = false @@ -1032,7 +1035,7 @@ python-versions = ">=3.6" [[package]] name = "pytz" -version = "2022.7.1" +version = "2023.3" description = "World timezone definitions, modern and historical" category = "main" optional = false @@ -1040,7 +1043,7 @@ python-versions = "*" [[package]] name = "pywin32" -version = "305" +version = "306" description = "Python for Window Extensions" category = "dev" optional = false @@ -1055,7 +1058,7 @@ optional = false python-versions = ">=3.7" [[package]] -name = "pyyaml" +name = "PyYAML" version = "6.0" description = "YAML parser and emitter for Python" category = "dev" @@ -1064,7 +1067,7 @@ python-versions = ">=3.6" [[package]] name = "pyzmq" -version = "25.0.0" +version = "25.0.2" description = "Python bindings for 0MQ" category = "dev" optional = false @@ -1101,7 +1104,7 @@ urllib3 = ">=1.21.1,<1.27" [package.extras] socks = ["PySocks (>=1.5.6,!=1.5.7)"] -use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] +use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"] [[package]] name = "rfc3339-validator" @@ -1124,7 +1127,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "selenium" -version = "4.8.2" +version = "4.8.3" description = "" category = "main" optional = false @@ -1137,7 +1140,7 @@ trio-websocket = ">=0.9,<1.0" urllib3 = {version = ">=1.26,<2.0", extras = ["socks"]} [[package]] -name = "send2trash" +name = "Send2Trash" version = "1.8.0" description = "Send file to trash natively under Mac OS X, Windows and Linux." category = "dev" @@ -1277,14 +1280,14 @@ sortedcontainers = "*" [[package]] name = "trio-websocket" -version = "0.9.2" +version = "0.10.2" description = "WebSocket library for Trio" category = "main" optional = false -python-versions = ">=3.5" +python-versions = ">=3.7" [package.dependencies] -async-generator = ">=1.10" +exceptiongroup = "*" trio = ">=0.11" wsproto = ">=0.14" @@ -1301,7 +1304,7 @@ dev = ["flake8 (<4.0.0)", "flake8-annotations", "flake8-bugbear", "flake8-commas [[package]] name = "urllib3" -version = "1.26.14" +version = "1.26.15" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = false @@ -1325,12 +1328,16 @@ python-versions = "*" [[package]] name = "webcolors" -version = "1.12" -description = "A library for working with color names and color values formats defined by HTML and CSS." +version = "1.13" +description = "A library for working with the color formats defined by HTML and CSS." category = "dev" optional = false python-versions = ">=3.7" +[package.extras] +docs = ["furo", "sphinx", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-notfound-page", "sphinxext-opengraph"] 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"sha256:75edcdc2f7d85b137124a6c3c9fc3933cdeaa12ecb9a6a959f22797a0feca7e1"}, - {file = "urllib3-1.26.14.tar.gz", hash = "sha256:076907bf8fd355cde77728471316625a4d2f7e713c125f51953bb5b3eecf4f72"}, + {file = "urllib3-1.26.15-py2.py3-none-any.whl", hash = "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"}, + {file = "urllib3-1.26.15.tar.gz", hash = "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305"}, ] wcwidth = [ {file = "wcwidth-0.2.6-py2.py3-none-any.whl", hash = "sha256:795b138f6875577cd91bba52baf9e445cd5118fd32723b460e30a0af30ea230e"}, {file = "wcwidth-0.2.6.tar.gz", hash = "sha256:a5220780a404dbe3353789870978e472cfe477761f06ee55077256e509b156d0"}, ] webcolors = [ - {file = "webcolors-1.12-py3-none-any.whl", hash = "sha256:d98743d81d498a2d3eaf165196e65481f0d2ea85281463d856b1e51b09f62dce"}, - {file = "webcolors-1.12.tar.gz", hash = "sha256:16d043d3a08fd6a1b1b7e3e9e62640d09790dce80d2bdd4792a175b35fe794a9"}, + {file = "webcolors-1.13-py3-none-any.whl", hash = "sha256:29bc7e8752c0a1bd4a1f03c14d6e6a72e93d82193738fa860cbff59d0fcc11bf"}, + {file = "webcolors-1.13.tar.gz", hash = "sha256:c225b674c83fa923be93d235330ce0300373d02885cef23238813b0d5668304a"}, ] webencodings = [ {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"}, diff --git a/pyproject.toml b/pyproject.toml index 3a337d3..a15cfdb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "mersearch" -version = "1.1.0" +version = "1.1.1" description = "" authors = ["jdkern11 "] readme = "README.md" @@ -25,6 +25,12 @@ optional = true [tool.poetry.group.notebook.dependencies] notebook = "^6.5.2" +[tool.poetry.group.chemistry] +optional = true + +[tool.poetry.group.chemistry.dependencies] +rdkit = "^2022.9.5" + [build-system] requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" diff --git a/tests/conf.py b/tests/conf.py index f3ca78b..5b71f02 100644 --- a/tests/conf.py +++ b/tests/conf.py @@ -4,18 +4,18 @@ from selenium.webdriver.firefox.service import Service from selenium.webdriver.firefox.options import Options -profile_path = str( - Path("~") - / "Library" - / "Application Support" - / "Firefox" - / "Profiles" - / "pwofczxw.default" -) +# profile_path = str( +# Path("~") +# / "Library" +# / "Application Support" +# / "Firefox" +# / "Profiles" +# / "pwofczxw.default" +# ) PROXY_HOST = "12.12.12.123" PROXY_PORT = "1234" options = Options() -options.set_preference("profile", profile_path) +# options.set_preference("profile", profile_path) options.set_preference("network.proxy.type", 1) options.set_preference("network.proxy.http", PROXY_HOST) options.set_preference("network.proxy.http_port", int(PROXY_PORT)) @@ -23,7 +23,8 @@ options.set_preference("useAutomationExtension", False) options.set_preference("excludeSwitches", "enable-automation") options.add_argument("--headless") -service = Service(r"/usr/local/bin/geckodriver") +path = Path.cwd() / '..' / 'data' / 'geckodriver' +service = Service(str(path)) configuration = {"service": service, "options": options} webdriver = webdriver.Firefox