Update ksrates to version 2.0.0

[Cecilia-Sensalari]

PR integrating code for version 2.0.0

Major updates:

• Implemented the reciprocal retention pipeline along side the existing whole-paranome and anchor pair Ks analyses (more details in our preprint and in the documentation)
• Nextflow pipeline ported to DSL2 syntax

Minor updates:

• Containers only supported for linux/amd64 platform and no longer for linux/arm64
• Upgraded Python package versions in requirements.txt
• Output prints an automatic interpretation of the Ks plot, namely which species share which WGMs with the focal species
• New command orthologs_ks_cleanup: deletes all ortholog BLAST tables from ortholog_distributions directory to free disk space; to be executed manually
• New command paralogs_ks_multi: executes the paralog Ks estimation for all species present in the Newick tree instead than for only the focal species; to be executed manually
• Nextflow template configuration file contains scope profiles to set up containers
• Test pipeline CI action generates downloadable output (the whole test/rate_adjustment/elaeis directory) to allow inspection of error logs and output files

[Copilot]

Copilot reviewed 76 out of 82 changed files in this pull request and generated no comments.

Files not reviewed (6)

• Dockerfile: Language not supported
• Singularity: Language not supported
• docs/concept.rst: Language not supported
• docs/configuration.rst: Language not supported
• docs/index.rst: Language not supported
• docs/input_output.rst: Language not supported

Comments suppressed due to low confidence (2)

docs/conf.py:4

• Ensure that the updated relative path correctly locates 'ksrates/_version.py' given the project structure; if the module location has also changed, update the accompanying comment accordingly.

p = os.path.abspath('..')

.github/workflows/test_pipeline.yml:40

• [nitpick] Confirm that the addition of the '--test' flag along with the new configuration file paths is intentional and aligns with the expected testing workflow to avoid unintended behavior in production runs.

NXF_VER=23.10.1 nextflow run ../main.nf --test --config config_files/config_elaeis.txt --expert config_files/config_expert.txt -with-docker ksrates

[Copilot]

Copilot reviewed 76 out of 82 changed files in this pull request and generated no comments.

Files not reviewed (6)

• Dockerfile: Language not supported
• Singularity: Language not supported
• docs/concept.rst: Language not supported
• docs/configuration.rst: Language not supported
• docs/index.rst: Language not supported
• docs/input_output.rst: Language not supported

Comments suppressed due to low confidence (3)

docs/conf.py:4

• The change from '../..' to '..' may cause an incorrect import of ksrates._version if the version file is still located two directories up. Please verify that the updated path matches the actual project structure.

p = os.path.abspath('..')

docs/conf.py:3

• There is a mismatch between the comment indicating a two-level up import path and the updated one-level up path in the code; consider updating the comment or the path to maintain consistency.

# Import version following relative path ../../ksrates/ksrates/_version.py

.github/workflows/test_pipeline.yml:40

• The addition of the '--test' flag alters the command behavior; please confirm that running Nextflow in test mode is intentional for the CI pipeline.

NXF_VER=23.10.1 nextflow run ../main.nf --test --config config_files/config_elaeis.txt --expert config_files/config_expert.txt -with-docker ksrates