chore!: remove functionality

bihealth · Jan 15, 2025 · 133bc87 · 133bc87
1 parent 900b67a
commit 133bc87
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diff --git a/docs_manual/index.rst b/docs_manual/index.rst
@@ -18,14 +18,12 @@ Manual
     | :ref:`Upload fastq files to SODAR <man_ingest_fastq>`
     | :ref:`Upload results of the Seasnap pipeline to SODAR <man_seasnap_itransfer_results>`
     | :ref:`Create a sample info file for Sea-snap <man_write_sample_info>`
-    | :ref:`Tools for archiving old projects <man_archive>`
 
 Use cases
     Use cases for common processing tasks.
 
     | :ref:`Exome sequencing <usecase_exomes>`
     | :ref:`Clinical single cell pipeline <usecase_single_cell>`
-    | :ref:`Archiving projects <usecase_archive>`
 
 Project Info
     More information on the project, including the changelog, list of contributing authors, and
@@ -56,7 +54,6 @@ Project Info
     man_ingest_fastq
     man_itransfer_results
     man_write_sample_info
-    man_archive
 
 .. toctree::
     :caption: Use Cases
@@ -66,7 +63,6 @@ Project Info
 
     usecase_exomes
     usecase_single_cell
-    usecase_archive_project
 
 .. toctree::
     :caption: Project Info

diff --git a/docs_manual/man_archive.rst b/docs_manual/man_archive.rst
diff --git a/docs_manual/usecase_archive_project.rst b/docs_manual/usecase_archive_project.rst
diff --git a/environment.yaml b/environment.yaml
@@ -9,7 +9,6 @@ dependencies:
   - python >=3.9
   - pip
   - uv >=0.5
-  - hashdeep
   - pysam >=0.22
   - vcfpy >=0.13.8
   - gcc_linux-64 >=13,<14

diff --git a/src/cubi_tk/__main__.py b/src/cubi_tk/__main__.py
@@ -12,8 +12,6 @@
 
 from cubi_tk import __version__
 
-from .archive import run as run_archive
-from .archive import setup_argparse as setup_argparse_archive
 from .common import run_nocmd
 from .irods import run as run_irods
 from .irods import setup_argparse as setup_argparse_irods
@@ -83,7 +81,6 @@ def setup_argparse():
     setup_argparse_sea_snap(
         subparsers.add_parser("sea-snap", help="Tools for supporting the RNA-SeASnaP pipeline.")
     )
-    setup_argparse_archive(subparsers.add_parser("archive", help="helper for archiving projects."))
 
     return parser, subparsers
 
@@ -118,7 +115,6 @@ def main(argv=None):
         "sodar": run_sodar,
         "irods": run_irods,
         "org-raw": run_org_raw,
-        "archive": run_archive,
     }
 
     res = cmds[args.cmd](args, parser, subparsers.choices[args.cmd] if args.cmd else None)

diff --git a/src/cubi_tk/archive/__init__.py b/src/cubi_tk/archive/__init__.py
diff --git a/src/cubi_tk/archive/classes.yaml b/src/cubi_tk/archive/classes.yaml