diff --git a/.github/workflows/run-pytest.yml b/.github/workflows/run-pytest.yml
index 489f0f6..1f6ffb6 100644
--- a/.github/workflows/run-pytest.yml
+++ b/.github/workflows/run-pytest.yml
@@ -11,7 +11,7 @@ jobs:
runs-on: ${{ matrix.os }}
strategy:
matrix:
- python-version: ["3.8", "3.12"]
+ python-version: ["3.8", "3.13"]
os: [ubuntu-latest]
steps:
diff --git a/README.md b/README.md
index 0b4d38d..d814bcd 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@
[](https://github.com/psf/black)
[](http://bioconda.github.io/recipes/geofetch/README.html)
-`geofetch` is a command-line tool that downloads sequencing data and metadata from GEO and SRA and creates [standard PEPs](https://pep.databio.org/). `geofetch` is hosted at [pypi](https://pypi.org/project/geofetch/). You can convert the result of geofetch into unmapped `bam` or `fastq` files with the included `sraconvert` command.
+**geofetch** is a command-line tool that downloads sequencing data and metadata from GEO and SRA and create metadata tables in [standard PEP format](https://pep.databio.org/). `geofetch` is hosted at [pypi](https://pypi.org/project/geofetch/). You can convert the result of geofetch into unmapped `bam` or `fastq` files with the included `sraconvert` command.
## Key geofetch features:
@@ -20,4 +20,44 @@
- Can search GEO to find relevant data
- Can be used either as a command-line tool or from within Python using an API
-For more information, see [complete documentation at geofetch.databio.org](http://geofetch.databio.org) (source in the [/docs](/docs) folder).
+## Docs
+
+---
+
+**Documentation**: https://pep.databio.org/geofetch/
+
+**Source Code**: https://github.com/pepkit/geofetch/
+
+---
+
+
+## Installation
+To install `geofetch` use this command:
+```
+pip install geofetch
+```
+or install the latest version from the GitHub repository:
+```
+pip install git+https://github.com/pepkit/geofetch.git
+```
+
+
+## How to cite:
+https://doi.org/10.1093/bioinformatics/btad069
+```bibtex
+@article{10.1093/bioinformatics/btad069,
+ author = {Khoroshevskyi, Oleksandr and LeRoy, Nathan and Reuter, Vincent P and Sheffield, Nathan C},
+ title = "{GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA}",
+ journal = {Bioinformatics},
+ volume = {39},
+ number = {3},
+ pages = {btad069},
+ year = {2023},
+ month = {03},
+ abstract = "{The Gene Expression Omnibus has become an important source of biological data for secondary analysis. However, there is no simple, programmatic way to download data and metadata from Gene Expression Omnibus (GEO) in a standardized annotation format.To address this, we present GEOfetch—a command-line tool that downloads and organizes data and metadata from GEO and SRA. GEOfetch formats the downloaded metadata as a Portable Encapsulated Project, providing universal format for the reanalysis of public data.GEOfetch is available on Bioconda and the Python Package Index (PyPI).}",
+ issn = {1367-4811},
+ doi = {10.1093/bioinformatics/btad069},
+ url = {https://doi.org/10.1093/bioinformatics/btad069},
+ eprint = {https://academic.oup.com/bioinformatics/article-pdf/39/3/btad069/49407404/btad069.pdf},
+}
+```
\ No newline at end of file
diff --git a/docs/img/geofetch_logo.svg b/docs/img/geofetch_logo.svg
new file mode 100644
index 0000000..372c82c
--- /dev/null
+++ b/docs/img/geofetch_logo.svg
@@ -0,0 +1,141 @@
+
+
+
+
diff --git a/geofetch/__init__.py b/geofetch/__init__.py
index fcd9139..2e3620e 100644
--- a/geofetch/__init__.py
+++ b/geofetch/__init__.py
@@ -1,12 +1,11 @@
""" Package-level data """
-import logmuse
import coloredlogs
+import logmuse
-from geofetch.geofetch import Geofetcher
-from geofetch.finder import Finder
from geofetch._version import __version__
-
+from geofetch.finder import Finder
+from geofetch.geofetch import Geofetcher
__author__ = ["Oleksandr Khoroshevskyi", "Vince Reuter", "Nathan Sheffield"]
__all__ = ["Finder", "Geofetcher", "__version__"]
diff --git a/geofetch/__main__.py b/geofetch/__main__.py
index 97e5466..077dace 100644
--- a/geofetch/__main__.py
+++ b/geofetch/__main__.py
@@ -1,4 +1,5 @@
import sys
+
from geofetch.geofetch import main
if __name__ == "__main__":
diff --git a/geofetch/_version.py b/geofetch/_version.py
index 8e2394f..6ece8ad 100644
--- a/geofetch/_version.py
+++ b/geofetch/_version.py
@@ -1 +1 @@
-__version__ = "0.12.6"
+__version__ = "0.12.7"
diff --git a/geofetch/cli.py b/geofetch/cli.py
index 6bb96b7..168b2a3 100644
--- a/geofetch/cli.py
+++ b/geofetch/cli.py
@@ -1,6 +1,8 @@
import argparse
import os
+
import logmuse
+
from geofetch._version import __version__
diff --git a/geofetch/finder.py b/geofetch/finder.py
index e41405e..587e1ae 100644
--- a/geofetch/finder.py
+++ b/geofetch/finder.py
@@ -1,19 +1,20 @@
+import logging
+import os
+import re
+from datetime import datetime, timedelta
+
+import coloredlogs
+import requests
+import xmltodict
+
from .const import (
- RETMAX,
- ETOOLS_GEO_GSE_BASE,
- ETOOLS_ENDING,
- TODAY_DATE,
DATE_FILTER,
+ ETOOLS_ENDING,
+ ETOOLS_GEO_GSE_BASE,
+ RETMAX,
THREE_MONTH_FILTER,
+ TODAY_DATE,
)
-import requests
-import xmltodict
-import re
-import os
-import logging
-import coloredlogs
-from datetime import datetime
-from datetime import timedelta
__author__ = "Oleksandr Khoroshevskyi"
diff --git a/geofetch/geofetch.py b/geofetch/geofetch.py
index bdbd6a1..b490428 100755
--- a/geofetch/geofetch.py
+++ b/geofetch/geofetch.py
@@ -1,65 +1,65 @@
import copy
import csv
+import logging
import os
+import re
import sys
+import time
+from typing import Dict, List, NoReturn, Tuple, Union
+
+import logmuse
+import pandas as pd
+import peppy
import requests
import xmltodict
import yaml
-import time
-import logging
-
from rich.progress import track
-import re
-import logmuse
from ubiquerg import expandpath
-from typing import List, Union, Dict, Tuple, NoReturn
-import peppy
-import pandas as pd
from geofetch.cli import _parse_cmdl
from geofetch.const import (
- GSE_PATTERN,
- SAMPLE_SUPP_METADATA_FILE,
+ CONFIG_PROCESSED_TEMPLATE_NAME,
+ CONFIG_RAW_TEMPLATE_NAME,
+ CONFIG_SRA_TEMPLATE,
EXP_SUPP_METADATA_FILE,
- NEW_GENOME_COL_NAME,
+ EXPERIMENT_PATTERN,
FILE_RAW_NAME_SAMPLE_PATTERN,
FILE_RAW_NAME_SUBSAMPLE_PATTERN,
- CONFIG_RAW_TEMPLATE_NAME,
- CONFIG_SRA_TEMPLATE,
- CONFIG_PROCESSED_TEMPLATE_NAME,
+ GSE_PATTERN,
+ NCBI_EFETCH,
+ NCBI_ESEARCH,
+ NEW_GENOME_COL_NAME,
NUM_RETRIES,
+ PROJECT_PATTERN,
+ SAMPLE_SUPP_METADATA_FILE,
SER_SUPP_FILE_PATTERN,
SUPP_FILE_PATTERN,
- PROJECT_PATTERN,
- NCBI_EFETCH,
- NCBI_ESEARCH,
- EXPERIMENT_PATTERN,
)
from geofetch.utils import (
Accession,
- build_prefetch_command,
- parse_accessions,
- parse_SOFT_line,
- convert_size,
- clean_soft_files,
- run_subprocess,
+ _check_file_existance,
+ _create_dot_yaml,
+ _dict_to_list_converter,
+ _filter_gsm,
_get_list_of_keys,
_get_value,
_read_tar_filelist,
- _check_file_existance,
- _separate_list_of_files,
- _update_columns,
- _sanitize_name,
_sanitize_config_string,
- _create_dot_yaml,
- _which,
- _dict_to_list_converter,
- _standardize_colnames,
+ _sanitize_name,
_separate_file_url,
- _filter_gsm,
+ _separate_list_of_files,
+ _standardize_colnames,
_unify_list_keys,
+ _update_columns,
+ _which,
+ build_prefetch_command,
+ clean_soft_files,
+ convert_size,
gse_content_to_dict,
is_prefetch_callable,
+ parse_accessions,
+ parse_SOFT_line,
+ run_subprocess,
)
_LOGGER = logging.getLogger(__name__)
diff --git a/geofetch/sraconvert.py b/geofetch/sraconvert.py
index d2dd3bc..6e64a9a 100755
--- a/geofetch/sraconvert.py
+++ b/geofetch/sraconvert.py
@@ -1,10 +1,11 @@
#!/usr/bin/env python
-from argparse import ArgumentParser
import os
-import pypiper
-import logmuse
import sys
+from argparse import ArgumentParser
+
+import logmuse
+import pypiper
__version__ = "0.1.0"
diff --git a/geofetch/utils.py b/geofetch/utils.py
index dcab44f..c006e7b 100644
--- a/geofetch/utils.py
+++ b/geofetch/utils.py
@@ -1,14 +1,15 @@
""" Independently-importable utilities to circumvent true scripts. """
+import csv
import logging
import os
+import re
import subprocess
import sys
-import re
-import requests
from io import StringIO
-import csv
-from typing import Union, List, NoReturn, Dict
+from typing import Dict, List, NoReturn, Union
+
+import requests
_LOGGER = logging.getLogger(__name__)
diff --git a/mkdocs.yml b/mkdocs.yml
deleted file mode 100644
index e8bc1b9..0000000
--- a/mkdocs.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-site_name: Geofetch
-site_url: http://code.databio.org/geofetch/
-repo_url: http://github.com/pepkit/geofetch
-site_logo: img/geofetch_logo_dark.svg
-pypi_name: geofetch
-paper_link: https://doi.org/10.1093/bioinformatics/btad069
-
-nav:
- - Getting started:
- - Introduction: README.md
- - Install and configure: install.md
- - SRA convert: sra_convert.md
- - Tutorials:
- - Tutorial for processed data: processed-data-downloading.md
- - Tutorial for raw data: raw-data-downloading.md
- - geofetch from within Python: python-usage.md
- - GSE Finder: gse_finder.md
- - How-to Guides:
- - Specifying samples to download: file-specification.md
- - Set SRA data download location: howto-location.md
- - Run SRA convert: how_to_convert_fastq_from_sra.md
- - Reference:
- - Metadata output: metadata_output.md
- - Usage: usage.md
- - FAQ: faq.md
- - Support: http://github.com/pepkit/geofetch/issues
- - Contributing: contributing.md
- - Changelog: changelog.md
-
-theme: databio
-
-
-plugins:
- - search
- - databio:
- jupyter_source: "docs_jupyter"
- jupyter_build: "docs_jupyter/build"
- usage_template: "docs/usage_template.md"
- usage_cmds:
- -"geofetch --help
diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
index 8cc987b..f9b4326 100644
--- a/requirements/requirements-all.txt
+++ b/requirements/requirements-all.txt
@@ -4,6 +4,6 @@ ubiquerg>=0.6.2
requests>=2.28.1
xmltodict>=0.13.0
pandas>=1.5.3
-peppy>=0.40.0
+peppy>=0.40.6
rich>=12.5.1
coloredlogs>=15.0.1
diff --git a/setup.py b/setup.py
index 2d180f2..4cd56f2 100644
--- a/setup.py
+++ b/setup.py
@@ -1,9 +1,10 @@
#! /usr/bin/env python
import os
-from setuptools import setup
import sys
+from setuptools import setup
+
PACKAGE = "geofetch"
REQDIR = "requirements"
@@ -49,6 +50,8 @@ def read_reqs(reqs_name):
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
+ "Programming Language :: Python :: 3.12",
+ "Programming Language :: Python :: 3.13",
"Topic :: Scientific/Engineering :: Bio-Informatics",
],
keywords="project, bioinformatics, sequencing, ngs, workflow, GUI",
diff --git a/tests/test_geofetch.py b/tests/test_geofetch.py
index 5e5d70f..e33fe0e 100644
--- a/tests/test_geofetch.py
+++ b/tests/test_geofetch.py
@@ -1,11 +1,12 @@
+import os
+import shutil
+
import peppy
+import pytest
import geofetch
from geofetch import Geofetcher, utils
from geofetch.utils import parse_accessions
-import os
-import pytest
-import shutil
INPUT_ACC_FILE = "tests/test_files/input_acc.txt"
GSE_FILES = "tests/test_files/soft_files"