diff --git a/README.md b/README.md index f96f5bd..7e4447e 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,15 @@ -# PPINet v0.1.0 +# PPI-net-builder v0.1.0 Protein-Protein Interaction (PPI) network construction and analysis using STRING-db (https://string-db.org/) in Python. ## Installation ```bash -pip install ppinet +pip install ppi-net-builder ``` ## Usage ```python -from ppinet import NetworkBuilder +from ppi_net_builder import NetworkBuilder genes = ["p53", "BRCA1", "cdk2", "Q99835"] annot_file_name = "./annotation.csv" # this will be created later diff --git a/ppi_net_builder/__init__.py b/ppi_net_builder/__init__.py new file mode 100644 index 0000000..a1e44a3 --- /dev/null +++ b/ppi_net_builder/__init__.py @@ -0,0 +1,5 @@ +from ppi_net_builder.src.data import DataManager +from ppi_net_builder.src.graph import NetworkBuilder + + +__version__ = "0.1.0" \ No newline at end of file diff --git a/ppinet/src/data.py b/ppi_net_builder/src/data.py similarity index 97% rename from ppinet/src/data.py rename to ppi_net_builder/src/data.py index e9efdb7..b0b435f 100644 --- a/ppinet/src/data.py +++ b/ppi_net_builder/src/data.py @@ -1,4 +1,4 @@ -from ppinet.src.fetch import fetch_string_ids +from ppi_net_builder.src.fetch import fetch_string_ids from enum import Enum import typing as t diff --git a/ppinet/src/fetch.py b/ppi_net_builder/src/fetch.py similarity index 100% rename from ppinet/src/fetch.py rename to ppi_net_builder/src/fetch.py diff --git a/ppinet/src/graph.py b/ppi_net_builder/src/graph.py similarity index 97% rename from ppinet/src/graph.py rename to ppi_net_builder/src/graph.py index d9d613d..62400fb 100644 --- a/ppinet/src/graph.py +++ b/ppi_net_builder/src/graph.py @@ -1,5 +1,5 @@ -from ppinet.src.data import DataManager -from ppinet.src.fetch import fetch_stringdb, fetch_enrichment, fetch_enrichment_figure +from ppi_net_builder.src.data import DataManager +from ppi_net_builder.src.fetch import fetch_stringdb, fetch_enrichment, fetch_enrichment_figure import pandas as pd import igraph as ig from igraph import Graph diff --git a/ppinet/__init__.py b/ppinet/__init__.py deleted file mode 100644 index 8722759..0000000 --- a/ppinet/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -from ppinet.src.data import DataManager -from ppinet.src.graph import NetworkBuilder - - -__version__ = "0.1.0" \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index c619001..3568a0c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ requires = ["setuptools>=61.0", "wheel"] build-backend = "setuptools.build_meta" [project] -name = "ppinet" +name = "ppi-net-builder" version = "0.1.0" description = "Protein-Protein Interaction (PPI) network construction and analysis using STRING-db (https://string-db.org/) in Python." readme = "README.md" @@ -24,7 +24,7 @@ dependencies = [ requires-python = ">=3.9" [project.urls] -Homepage = "https://github.com/qwerty239qwe/ppinet" +Homepage = "https://github.com/qwerty239qwe/ppi_net_builder" [tool.bumpver] current_version = "0.1.0" diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..20a449e --- /dev/null +++ b/requirements.txt @@ -0,0 +1,36 @@ +# +# This file is autogenerated by pip-compile with Python 3.10 +# by the following command: +# +# pip-compile pyproject.toml +# +certifi==2024.12.14 + # via requests +charset-normalizer==3.4.1 + # via requests +colorama==0.4.6 + # via tqdm +idna==3.10 + # via requests +igraph==0.11.8 + # via ppipy (pyproject.toml) +numpy==2.2.1 + # via pandas +pandas==2.2.3 + # via ppipy (pyproject.toml) +python-dateutil==2.9.0.post0 + # via pandas +pytz==2024.2 + # via pandas +requests==2.32.3 + # via ppipy (pyproject.toml) +six==1.17.0 + # via python-dateutil +texttable==1.7.0 + # via igraph +tqdm==4.67.1 + # via ppipy (pyproject.toml) +tzdata==2024.2 + # via pandas +urllib3==2.3.0 + # via requests