diff --git a/bioflow/cli.py b/bioflow/cli.py index fe8faf03..ebb197dc 100755 --- a/bioflow/cli.py +++ b/bioflow/cli.py @@ -27,6 +27,7 @@ def main(): def initialize(path, neo4jserver, mongoserver): """ Initialized the working environement + \f :param path: path where the external data sources are expected to be stored :param neo4jserver: neo4j server adress and port @@ -46,6 +47,7 @@ def initialize(path, neo4jserver, mongoserver): def downloaddbs(): """ Downloads the databases automatically + \f :return: """ @@ -58,6 +60,7 @@ def downloaddbs(): def setorg(organism): """ Sets organism-specific configurations + \f :param organism: :return: @@ -73,6 +76,7 @@ def setorg(organism): def purgeneo4j(): """ Wipes the neo4j organism-specific database + \f :return: """ @@ -88,6 +92,7 @@ def purgeneo4j(): def loadneo4j(): """ Loads the information from external database into the master repositry inside neo4j + \f :return: """ @@ -110,6 +115,8 @@ def sethits(source, background): are HGCN gene names (TP53), Uniprot gene names (P53_HUMAN) or Uniprot Accession numbers ( P04637). Other sources, such as ENSEMBL or PDB IDs. + \f + :param source: :param background: :return: @@ -122,6 +129,8 @@ def sethits(source, background): def rebuildlaplacians(): """ Extracts the Laplacian matrices from the master graph database. + \f + :return: """ from bioflow.utils.top_level import rebuild_the_laplacians @@ -136,6 +145,7 @@ def rebuildlaplacians(): def purgemongo(collection): """ purges the mongodb collection currently used to store all the information. + \f :param collection: :return: @@ -159,6 +169,7 @@ def purgemongo(collection): def interactomeanalysis(depth, processors, skipsampling, skiphitflow): """ Performs interactome analysis given background set given earlier. + \f :param depth: :param processors: @@ -187,6 +198,7 @@ def interactomeanalysis(depth, processors, skipsampling, skiphitflow): def knowledgeanalysis(depth, processors, skipsampling): """ Performs annotome analysis given background set given earlier. + \f :param depth: :param processors: diff --git a/requirements.txt b/requirements.txt index 44ed4e3f..d7909f59 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,7 +5,7 @@ scikit-learn < 0.17 cython < 0.23 pymongo < 4.0 requests < 3.0 -click < 6.0 +click < 8.0 scikits.sparse < 0.3 mock < 2.0 requests-ftp < 0.4 diff --git a/setup.py b/setup.py index a9bc949b..785c38a7 100755 --- a/setup.py +++ b/setup.py @@ -24,7 +24,7 @@ 'cython < 0.23', 'pymongo < 4.0', 'requests < 3.0', - 'click < 6.0', + 'click < 8.0', 'scikits.sparse < 0.3', 'mock < 2.0', 'requests-ftp < 0.4', @@ -35,7 +35,7 @@ requirements = [ 'pymongo < 4.0', 'requests < 3.0', - 'click < 6.0', + 'click < 8.0', 'requests-ftp < 0.4', 'neo4j-driver < 1.6', ]