Merge pull request #29 from mbhall88/feat/force-ignore

feat: rework force and ignore

.github/workflows/fastq-dl.yml

@@ -40,6 +40,7 @@ jobs:
         run: |
           fastq-dl --version
           fastq-dl --help
+          just test --verbosity=2
 
       - name: Test ENA Download
         run: |

CHANGELOG.md

@@ -7,6 +7,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### TODO
+
+- rework version to centralize it to the `pyproject.toml` file
+- lint
+- consider refactoring more
+- consider adding back aspera support (now available from bioconda)
+- major bump in version
+
+### Added
+
+- `--ignore` to ignore MD5 checksums
+
+### Changed
+
+- (**BREAKING**) the `--force` flag now overwrites existing files, but will check the MD5
+  checksums of the downloaded files. Previously, it would force download the file, but
+  ignore the MD5 as well. See https://github.com/rpetit3/fastq-dl/issues/21#issuecomment-2190686184
+  for more details. Use the newly added `--ignore` flag to ignore MD5 checksums too.
+
 ## [2.0.4]
 
 ### Fixed

fastq_dl/__init__.py

@@ -0,0 +1,11 @@
+from pathlib import Path
+from typing import Union
+
+PROGRAM = "fastq-dl"
+VERSION = "2.0.4"
+ENA_FAILED = "ENA_NOT_FOUND"
+SRA_FAILED = "SRA_NOT_FOUND"
+SRA = "SRA"
+ENA = "ENA"
+ENA_URL = "https://www.ebi.ac.uk/ena/portal/api/search?result=read_run&format=tsv"
+PathLike = Union[str, Path]