remove amdirt capitalization

.github/workflows/ci_test.yml

@@ -1,4 +1,4 @@
-name: AMDirT-CI
+name: amdirt-CI
 
 on: [push, pull_request]
 

.github/workflows/publish_pypi.yml

@@ -13,8 +13,8 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v3
         with:
-          python-version: "3.9"
-      - name: Build AMDirT
+          python-version: "3.12"
+      - name: Build amdirt
         run: |
           pip install wheel
           python setup.py sdist bdist_wheel

AMDirT/__init__.py

@@ -1 +1 @@
-__version__ = "1.6.3"
+__version__ = "1.6.4"

AMDirT/assets/tables.json

@@ -3,24 +3,24 @@
     "ancientmetagenome-environmental": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv",
     "ancientmetagenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv",
     "ancientsinglegenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv",
-    "test": "https://raw.githubusercontent.com/SPAAM-community/AMDirT/dev/tests/data/valid.tsv"
+    "test": "https://raw.githubusercontent.com/SPAAM-community/amdirt/dev/tests/data/valid.tsv"
   },
   "samples_schema": {
     "ancientmetagenome-environmental": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples_schema.json",
     "ancientmetagenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples_schema.json",
     "ancientsinglegenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples_schema.json",
-    "test": "https://raw.githubusercontent.com/SPAAM-community/AMDirT/dev/tests/data/schema.json"
+    "test": "https://raw.githubusercontent.com/SPAAM-community/amdirt/dev/tests/data/schema.json"
   },
   "libraries": {
     "ancientmetagenome-environmental": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv",
     "ancientmetagenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv",
     "ancientsinglegenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv",
-    "test": "https://raw.githubusercontent.com/SPAAM-community/AMDirT/dev/tests/data/valid_libaries.tsv"
+    "test": "https://raw.githubusercontent.com/SPAAM-community/amdirt/dev/tests/data/valid_libaries.tsv"
   },
   "libraries_schema": {
     "ancientmetagenome-environmental": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries_schema.json",
     "ancientmetagenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries_schema.json",
     "ancientsinglegenome-hostassociated": "https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries_schema.json",
-    "test": "https://raw.githubusercontent.com/SPAAM-community/AMDirT/dev/tests/data/libraries_schema.json"
+    "test": "https://raw.githubusercontent.com/SPAAM-community/amdirt/dev/tests/data/libraries_schema.json"
   }
 }

AMDirT/autofill/__init__.py

@@ -1,7 +1,7 @@
-from AMDirT.validate.domain import DatasetValidator
-from AMDirT.core import get_json_path, logger
-from AMDirT.core.ena import ENAPortalAPI
-from AMDirT.validate.exceptions import NetworkError
+from amdirt.validate.domain import DatasetValidator
+from amdirt.core import get_json_path, logger
+from amdirt.core.ena import ENAPortalAPI
+from amdirt.validate.exceptions import NetworkError
 import json
 
 import sys

AMDirT/cli.py

@@ -1,13 +1,13 @@
 import click
-from AMDirT import __version__
-
-from AMDirT.validate import run_validation
-from AMDirT.viewer import run_app
-from AMDirT.convert import run_convert
-from AMDirT.core import get_json_path, get_amdir_tags, get_latest_tag
-from AMDirT.autofill import run_autofill
-from AMDirT.merge import merge_new_df
-from AMDirT.download import download as download_amdir
+from amdirt import __version__
+
+from amdirt.validate import run_validation
+from amdirt.viewer import run_app
+from amdirt.convert import run_convert
+from amdirt.core import get_json_path, get_amdir_tags, get_latest_tag
+from amdirt.autofill import run_autofill
+from amdirt.merge import merge_new_df
+from amdirt.download import download as download_amdir
 from json import load
 
 
@@ -49,9 +49,9 @@ def get_table_list():
 @click.option("--verbose", is_flag=True, help="Verbose mode")
 def cli(ctx, verbose, no_args_is_help=True, **kwargs):
     """\b
-    AMDirT: Performs validity check of AncientMetagenomeDir datasets
-    Authors: AMDirT development team and the SPAAM community
-    Homepage & Documentation: https://github.com/SPAAM-community/AMDirT
+    amdirt: Performs validity check of AncientMetagenomeDir datasets
+    Authors: amdirt development team and the SPAAM community
+    Homepage & Documentation: https://github.com/SPAAM-community/amdirt
     \b
     """
     ctx.ensure_object(dict)
@@ -330,7 +330,7 @@ def merge(ctx, no_args_is_help=True, **kwargs):
 )
 def download(no_args_is_help=True, **kwargs):
     """\b
-    Download a table from the AMDirT repository
+    Download a table from the amdirt repository
     """
     download_amdir(**kwargs)
 

AMDirT/convert/__init__.py

@@ -1,6 +1,6 @@
 from sys import path
 import os
-from AMDirT.core import (
+from amdirt.core import (
     prepare_accession_table,
     prepare_bibtex_file,
     prepare_eager_table,
@@ -12,10 +12,10 @@
     get_remote_resources,
     get_json_path,
 )
-from AMDirT.validate import AMDirValidator
-from AMDirT.validate.exceptions import DatasetValidationError
+from amdirt.validate import AMDirValidator
+from amdirt.validate.exceptions import DatasetValidationError
 from json import load
-from AMDirT.core import logger
+from amdirt.core import logger
 import pandas as pd
 import warnings
 
@@ -38,7 +38,7 @@ def run_convert(
     mag=False,
     verbose=False,
 ):
-    """Run the AMDirT conversion application to input samplesheet tables for different pipelines
+    """Run the amdirt conversion application to input samplesheet tables for different pipelines
 
     Args:
         samples (str): Path to AncientMetagenomeDir filtered samples tsv file

AMDirT/core/__init__.py

@@ -22,7 +22,7 @@
     colorlog.ColoredFormatter("%(log_color)s%(name)s [%(levelname)s]: %(message)s")
 )
 
-logger = colorlog.getLogger("AMDirT")
+logger = colorlog.getLogger("amdirt")
 logger.addHandler(handler)
 logger.propagate = False
 
@@ -44,7 +44,7 @@ def monkeypatch_get_storage_manager():
 
 
 def get_json_path():
-    path = get_module_dir("AMDirT.assets").joinpath("tables.json")
+    path = get_module_dir("amdirt.assets").joinpath("tables.json")
     return path
 
 

AMDirT/core/ena.py

@@ -1,5 +1,5 @@
 import requests
-from AMDirT.core import logger
+from amdirt.core import logger
 import os
 from typing import List, Dict
 

AMDirT/download/__init__.py

@@ -1,4 +1,4 @@
-from AMDirT.core import (
+from amdirt.core import (
     logger,
     get_amdir_tags,
     get_remote_resources,
@@ -9,7 +9,7 @@
 
 def download(table: str, table_type: str, release: str, output: str = ".") -> str:
     """
-    Download a table from the AMDirT repository.
+    Download a table from the amdirt repository.
 
     Parameters
     ----------

AMDirT/merge/__init__.py

@@ -1,8 +1,8 @@
-from AMDirT.validate.application import AMDirValidator
-from AMDirT.validate.exceptions import DatasetValidationError
+from amdirt.validate.application import AMDirValidator
+from amdirt.validate.exceptions import DatasetValidationError
 import warnings
 import pandas as pd
-from AMDirT.core import logger, get_remote_resources
+from amdirt.core import logger, get_remote_resources
 from os.path import join
 
 

AMDirT/validate/__init__.py

@@ -1,4 +1,4 @@
-from AMDirT.validate.application import AMDirValidator
+from amdirt.validate.application import AMDirValidator
 import warnings
 
 def run_validation(

AMDirT/validate/application/__init__.py

@@ -1,8 +1,8 @@
 from typing import Iterable, AnyStr, Union
-from AMDirT.validate.domain import DatasetValidator, DFError
-from AMDirT.core import get_json_path
-from AMDirT.core.diff import get_sample_diff
-from AMDirT.core.ena import ENAPortalAPI
+from amdirt.validate.domain import DatasetValidator, DFError
+from amdirt.core import get_json_path
+from amdirt.core.diff import get_sample_diff
+from amdirt.core.ena import ENAPortalAPI
 from rich.progress import track
 from pathlib import Path
 import pandas as pd

AMDirT/validate/domain/__init__.py

@@ -1,7 +1,7 @@
 import json
 import pandas as pd
-from AMDirT.validate import exceptions
-from AMDirT.core import logger
+from amdirt.validate import exceptions
+from amdirt.core import logger
 from io import StringIO
 from pathlib import Path
 from rich.table import Table
@@ -291,7 +291,7 @@ def to_rich(self):
         """
 
         table = Table(
-            title=f"AMDirT Validation Report of {self.dataset_name} against {self.schema_name}"
+            title=f"amdirt Validation Report of {self.dataset_name} against {self.schema_name}"
         )
         columns = ["Error", "Source", "Column", "Row", "Message"]
         for column in columns:

AMDirT/viewer/__init__.py

@@ -1,15 +1,15 @@
-# from AMDirT import logger
+# from amdirt import logger
 from distutils.log import warn
 import sys
 from streamlit.web import cli as stcli
 from pathlib import Path
-from AMDirT.core import get_json_path, logger
+from amdirt.core import get_json_path, logger
 import warnings
 
 
 def run_app(tables=None, verbose=False):
     """
-    Run the AMDirT interactive filtering application
+    Run the amdirt interactive filtering application
 
     Args:
         tables (str): path to JSON file listing AncientMetagenomeDir tables
@@ -32,5 +32,5 @@ def run_app(tables=None, verbose=False):
         "--config", 
         config_path
     ]
-    logger.info("\n[AMDirT] To close app, press on your keyboard: ctrl+c\n")
+    logger.info("\n[amdirt] To close app, press on your keyboard: ctrl+c\n")
     sys.exit(stcli.main())

AMDirT/viewer/streamlit.py

@@ -6,8 +6,8 @@
 import zipfile
 import json
 import os
-from AMDirT import __version__
-from AMDirT.core import (
+from amdirt import __version__
+from amdirt.core import (
     prepare_bibtex_file,
     prepare_eager_table,
     prepare_mag_table,
@@ -22,7 +22,7 @@
 
 
 st.set_page_config(
-    page_title="AMDirT viewer",
+    page_title="amdirt viewer",
     page_icon="https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/assets/images/logos/spaam-AncientMetagenomeDir_logo_mini.png",
     layout="wide",
 )
@@ -68,7 +68,7 @@ def parse_args():
 """,
         unsafe_allow_html=True,
     )
-    st.write(f"# [AMDirT](https://github.com/SPAAM-community/AMDirT) viewer tool")
+    st.write(f"# [amdirt](https://github.com/SPAAM-community/amdirt) viewer tool")
     st.write(f"\n Version: {__version__}")
     st.session_state.tag_name = st.selectbox(
         label="Select an AncientMetagenomeDir release", options=tags

README.md

@@ -1,20 +1,20 @@
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4003825.svg)](https://doi.org/10.5281/zenodo.4003825) [![PyPI version](https://badge.fury.io/py/AMDirT.svg)](https://pypi.org/project/AMDirT) [![Documentation Status](https://readthedocs.org/projects/amdirt/badge/?version=dev)](https://amdirt.readthedocs.io/en/dev/?badge=dev) [![AMDirT-CI](https://github.com/SPAAM-community/AMDirT/actions/workflows/ci_test.yml/badge.svg)](https://github.com/SPAAM-community/AMDirT/actions/workflows/ci_test.yml)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4003825.svg)](https://doi.org/10.5281/zenodo.4003825) [![PyPI version](https://badge.fury.io/py/amdirt.svg)](https://pypi.org/project/amdirt) [![Documentation Status](https://readthedocs.org/projects/amdirt/badge/?version=dev)](https://amdirt.readthedocs.io/en/dev/?badge=dev) [![amdirt-CI](https://github.com/SPAAM-community/amdirt/actions/workflows/ci_test.yml/badge.svg)](https://github.com/SPAAM-community/amdirt/actions/workflows/ci_test.yml)
 
   <picture>
-    <img alt="AMDirT Logo" src="https://raw.githubusercontent.com/SPAAM-community/AMDirT/master/assets/logo_rectangular_transparent.png">
+    <img alt="amdirt Logo" src="https://raw.githubusercontent.com/SPAAM-community/amdirt/master/assets/logo_rectangular_transparent.png">
   </picture>
 
-**AMDirT**: [**A**ncient**M**etagenome**Dir**](https://github.com/SPAAM-community/ancientmetagenomedir) **T**oolkit
+**amdirt**: [**A**ncient**M**etagenome**Dir**](https://github.com/SPAAM-community/ancientmetagenomedir) **T**oolkit
 
-AMDirT is a toolkit for interacting with the AncientMetagenomeDir metadata repository of ancient metagenomic samples and ancient microbial genomes.
+amdirt is a toolkit for interacting with the AncientMetagenomeDir metadata repository of ancient metagenomic samples and ancient microbial genomes.
 
 This tool provides ways to explore and download sequencing data for ancient microbial and environmental (meta)genomes, automatically prepare input samplesheets for a range of bioinformatic processing pipelines, and to validate AncientMetagenomeDir submissions.
 
 For documentation on using the tool, please see [How Tos](https://amdirt.readthedocs.io/en/latest/how_to/index.html), [Tutorials](https://amdirt.readthedocs.io/en/latest/tutorials/index.html) and/or [Quick Reference](https://amdirt.readthedocs.io/en/latest/reference.html).
 
 ## Install
 
-AMDirT has been tested on different Unix systems (macOS and Ubuntu) using Intel and AMD chips. If you suspect that AMDirT isn't working properly because you use a different hardware/OS, please open an [issue on GitHub](https://github.com/SPAAM-community/AMDirT/issues).
+amdirt has been tested on different Unix systems (macOS and Ubuntu) using Intel and AMD chips. If you suspect that amdirt isn't working properly because you use a different hardware/OS, please open an [issue on GitHub](https://github.com/SPAAM-community/amdirt/issues).
 
 ### 1. With [pip](https://pip.pypa.io/en/stable/getting-started/)
 
@@ -24,7 +24,7 @@ pip install amdirt
 
 ### 2. With conda
 
-Installing AMDirT in a dedicated [conda](https://docs.conda.io/projects/miniconda/en/latest/index.html) environment
+Installing amdirt in a dedicated [conda](https://docs.conda.io/projects/miniconda/en/latest/index.html) environment
 
 ```bash
 conda create -n amdirt -c bioconda amdirt #install amdirt in a dedicated conda environment
@@ -36,13 +36,13 @@ conda deactivate amdirt # deactivate the conda environment
 ### The latest development version, directly from GitHub
 
 ```bash
-pip install --upgrade --force-reinstall git+https://github.com/SPAAM-community/AMDirT.git@dev
+pip install --upgrade --force-reinstall git+https://github.com/SPAAM-community/amdirt.git@dev
 ```
 
 ### The latest development version, with local changes
 
-- Fork AMDirT on GitHub
-- Clone your fork `git clone [your-AMDirT-fork]`
+- Fork amdirt on GitHub
+- Clone your fork `git clone [your-amdirt-fork]`
 - Checkout the `dev` branch `git switch dev`
 - Create the conda environment `conda env create -f environment.yml`
 - Activate the environment `conda activate amdirt`
@@ -58,20 +58,20 @@ To locally render documentation:
 
 ## Cite
 
-AMDirT has been published in F1000 with the following _DOI_: [10.12688/f1000research.134798.2](https://doi.org/10.12688/f1000research.134798.2).  
+amdirt has been published in F1000 with the following _DOI_: [10.12688/f1000research.134798.2](https://doi.org/10.12688/f1000research.134798.2).  
 
-You can cite AMDirT like so:
+You can cite amdirt like so:
 
 ```
-Borry M, Forsythe A, Andrades Valtueña A et al. Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT. F1000Research 2024, 12:926
+Borry M, Forsythe A, Andrades Valtueña A et al. Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with amdirt. F1000Research 2024, 12:926
 ```
 
 A bibtex file is also available here: [amdirt.bib](amdirt.bib)
 
 
 ## More information
 
-For more information, please see the AMDirT Documentation
+For more information, please see the amdirt Documentation
 
 - Stable: [amdirt.readthedocs.io/en/latest/](https://amdirt.readthedocs.io/en/latest/)
 - Development version: [amdirt.readthedocs.io/en/dev/](https://amdirt.readthedocs.io/en/dev/)