diff --git a/README.rst b/README.rst index bb2c5dee..ffbff0ef 100644 --- a/README.rst +++ b/README.rst @@ -83,7 +83,7 @@ You can install both :code:`graph-tool` and the Facebook :code:`Faiss` library b :: - conda create --name -c conda-forge graph-tool faiss python= + conda create --name -c conda-forge graph-tool==2.37 faiss python= conda activate diff --git a/cord19kg/examples/notebooks/Glucose is a risk facor for COVID-19 (3000 papers).ipynb b/cord19kg/examples/notebooks/Glucose is a risk facor for COVID-19 (3000 papers).ipynb index 9d8a7d4b..8ddd8620 100644 --- a/cord19kg/examples/notebooks/Glucose is a risk facor for COVID-19 (3000 papers).ipynb +++ b/cord19kg/examples/notebooks/Glucose is a risk facor for COVID-19 (3000 papers).ipynb @@ -21,7 +21,7 @@ "!echo \"deb http://downloads.skewed.de/apt bionic main\" >> /etc/apt/sources.list\n", "!apt-key adv --keyserver keys.openpgp.org --recv-key 612DEFB798507F25\n", "!apt-get update\n", - "!apt-get install python3-graph-tool python3-cairo python3-matplotlib\n", + "!apt-get install python3-graph-tool=2.37 python3-cairo python3-matplotlib\n", "\n", "DATA_PATH = \"BlueGraph/cord19kg/examples/data/\"" ] @@ -46,7 +46,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -70,17 +70,9 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Data path: '../data/'\n" - ] - } - ], + "outputs": [], "source": [ "try:\n", " print(f\"Data path: '{DATA_PATH}'\")\n", @@ -91,7 +83,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -110,7 +102,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -123,21 +115,9 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Downloading the file to '../data/Glucose_risk_3000_papers.csv.zip'\n", - "Decompressing ...\n", - "Done.\n", - "CPU times: user 4.04 s, sys: 413 ms, total: 4.45 s\n", - "Wall time: 7.08 s\n" - ] - } - ], + "outputs": [], "source": [ "%%time\n", "download_from_nexus(\n", @@ -151,91 +131,9 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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124737supercomplex i+iiinadh dehydrogenase (ubiquinone)http://purl.obolibrary.org/obo/NCIT_C118184A complex of over 40 proteins found in the inn...[('http://purl.obolibrary.org/obo/NCIT_C21176'...
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44527geometric distortiongeometric distributionhttp://purl.obolibrary.org/obo/NCIT_C53211A discrete, statistical distribution which is ...[('http://purl.obolibrary.org/obo/NCIT_C53207'...
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3Surfactant protein-D and pulmonary host defenseCrouch, Erika CSurfactant protein-D (SP-D) participates in th...10.1186/rr19https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5...Respir ResPMC5954911667972.02000-08-25
56CLINICAL VIGNETTESNaNNaN10.1046/j.1525-1497.18.s1.20.xhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1...J Gen Intern MedPMC149498812753119.02003-04-01
58Clinical VignettesNaNNaN10.1046/j.1525-1497.2001.0160s1023.xhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1...J Gen Intern MedPMC149531611357836.02001-04-01
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" - ], - "text/plain": [ - " title authors \\\n", - "id \n", - "3 Surfactant protein-D and pulmonary host defense Crouch, Erika C \n", - "56 CLINICAL VIGNETTES NaN \n", - "58 Clinical Vignettes NaN \n", - "\n", - " abstract \\\n", - "id \n", - "3 Surfactant protein-D (SP-D) participates in th... \n", - "56 NaN \n", - "58 NaN \n", - "\n", - " doi \\\n", - "id \n", - "3 10.1186/rr19 \n", - "56 10.1046/j.1525-1497.18.s1.20.x \n", - "58 10.1046/j.1525-1497.2001.0160s1023.x \n", - "\n", - " url journal \\\n", - "id \n", - "3 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5... Respir Res \n", - "56 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1... J Gen Intern Med \n", - "58 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1... J Gen Intern Med \n", - "\n", - " pmc_id pubmed_id publish_time \n", - "id \n", - "3 PMC59549 11667972.0 2000-08-25 \n", - "56 PMC1494988 12753119.0 2003-04-01 \n", - "58 PMC1495316 11357836.0 2001-04-01 " - ] - }, - "execution_count": 27, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "paper_medata = download_from_nexus(uri=f\"{nexus_endpoint}/resources/{nexus_bucket}/_/8fc1e60c-1ebe-4173-82c0-9775a4917041\",\n", " output_path = DATA_PATH, config_file_path=nexus_config_file, nexus_endpoint=nexus_endpoint, nexus_bucket=nexus_bucket)\n", @@ -1276,7 +586,7 @@ }, { "cell_type": "code", - "execution_count": 28, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -1296,7 +606,7 @@ }, { "cell_type": "code", - "execution_count": 29, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -1343,7 +653,7 @@ }, { "cell_type": "code", - "execution_count": 30, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -1368,32 +678,11 @@ }, { "cell_type": "code", - "execution_count": 31, + "execution_count": null, "metadata": { "scrolled": false }, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - " \n", - " " - ], - "text/plain": [ - "" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "outputs": [], "source": [ "visualization_app.run(port=8081, mode=\"inline\")" ] @@ -1407,11 +696,11 @@ }, { "cell_type": "code", - "execution_count": 32, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ - "# visualization_app.run(port=8081, mode=\"external\")" + "visualization_app.run(port=8081, mode=\"external\")" ] } ], diff --git a/setup.py b/setup.py index aba7cbab..d7b281ed 100644 --- a/setup.py +++ b/setup.py @@ -67,7 +67,7 @@ "dev": [ "tox", "pytest", "pytest-bdd", "pytest-cov==2.10.1", "pytest-mock==3.3.1", "codecov", - "dash", + "dash==1.19.0", "jupyter_dash", "dash_bootstrap_components", "dash_daq", @@ -81,7 +81,7 @@ ], "docs": [ "sphinx", "sphinx-bluebrain-theme", - "dash", + "dash==1.19.0", "jupyter_dash" # a temporary solution, mocking this module fails ], "cord19kg": [