* Rename parameter "max_number_outgroups"
* Rename parameter (consensus multiple outgroups)
* Rename parameter (y_axis_max_limit_paralogs_plot)
* Rename parameter (max_ks_paralogs)
* Rename parameter (max_ks_orthologs)
* Rename parameter (collinearity)
* Rename parameter (bin_width_paralogs)
* Rename parameter (bin_width_orthologs)

* Rename headers of both adjustment table files
* Rename header "Focal_Species" in trios file
* Rename ortholog DB header, remove DB median data
* Add adjust. table description in input_output.rst
* Add subsections in output file list (docs)

* Add interactive container for manual pipeline
* Mounting Windows filesystem in WSL2
- Explain how to access the Windows
file system from the WSL2 terminal,
which by default is initialized in the
Linux home.
- Singularity commands in WSL2 need to
manually mount the Windows file system
within the container.

- First install non-Python dependencies and
lastly the package itself (with pip3)
- Add "sudo apt-get update" in step 1
- Add install python3-pip (for pip3) in step 1
- Remove redundant link to paml docs
- Fuse the cloning and pip3 steps in one step

* WSL2: manual mounting of Windows filesystem
- Add note about how to mount the Windows
file system in the WSL2 terminal, which is
initialized by default in the Linux home.

- The legend of multi-panel figures of ELMM
models has now for each component a left handle
(solid line) and a right handle (dotted line)
to refer to the fitted and initialized component.
- The total probability (black line) and the
histogram have a single handle aligned to right.

* Update y-axis label for weighted data
* Adjust default fontsizes in ks.mplstyle
* Legend default fontsize set to 14

- If there are missing species pairs in the DBs,
generate a PDF figure only if at least one trio has
complete data (Ks list and Ks peak estimate).
- Log warnings when skipping a trio due to
missing data in DBs.
- The missing pairs are listed at the end, as
missing 1) from both databases, 2) from only 
peak DB and 3) from only Ks list DB.
- Note: if the ortholog peak DB isn't present but
the Ks list DB is complete, the distributions
will still be plotted, all without their modes.

* Change PAML installation (from source)
* Paml instructions in installation.rst
* Improve container docs (installation.rst)
* Update comments in Dockerfile and Singularity file
* Remove squared brakets in NF command
* Rename Paralog --> Ortholog in ortholog TSV file
* Remove redundant color argument in modeling.py
* Update to tool name "ksrates" in the license
* Rename "wgd" module to "wgd_ksrates"
* Replace "wgd" with "wgd_ksrates" in container file
* Update license (author and year)
* Update installation.rst (link to singularity docs)
* Add note in local installation about Windows users
* Remove installation commands through bioconda

PDF with ortholog distributions has now one row instead of two
The mean median line is removed
The mean mode line now doesn't span anymore the whole y-axis but stops before the legend box

- The convergence threshold is now 
the same for ELMM (1e-6).
- If not converged after 300 iterations,
write NA in the result table.

* Update concept.rst
* Update input_output.rst
* Update usage.rst (file paths and descriptions)
* Delete .buildinfo
* Describe ks.tsv file format
* Add (E)LMM file format description; internal links
* Add (E)LMM file figures
* Rename header in ELMM TSV file
* Restructure mixture model section and add table
* Reduce paralog analyses description in docs
* Add Note block in input_output.rst about filenames
* Rename header in main.nf
* Add preprint DOI in "How to cite us" doc page
* Replace <focal species> with species (filename)

* Ks plot without divergence lines has inner legend
* Anchor cluster plot without lines has inner legend
* Exp-log plot without lines has inner legend
* Lognormal plot without lines has inner legend
* Reduce right margin of simple plots
* Ask matplotlib>=3.3.3 to fix a compatibility issue

* Anchor weights (also in paralogs-analyses command)
* Set the number of components to 3 in test dataset
* Rename function in anchor weighting
* Move compute_weight; del 0.05 in ks_list_from_tsv

* Rename with 'focal species'
Rename 'species of interest' and 'main species' in documentation RST files,
function docstrings, comments in code, in config_elaeis.txt, but also
in some actual code lines: in generate_config.py and fc_configfile.py
('focal_species' field), in main.nf (parse config file in setup process).

* renaming gff_filename field
* Rename (adjustment arrows, bootstrap iterations)
* Improve parameter description in configuration.rst
* Rename "adjustment" in filenames and python output
* Rename rates: branch contribution or ks distances
* Rename "adjustment" (leftover)

* Describe logging level in configuration.rst

* Add database names in input_output.rst

* Rename peak_stats
* Rename focal species in readme

* Catch missing species in fasta_filenames
* Catch missing species in latin_names and exit
* Bugfix for catch missing species in latin_names
* Bugifx to catch missing species in latin_names

* Rename max_mixture_model_ks

* Add parameter default values in configuration.rst

* Correct RST syntax

* Add output directory and filenames to docs

* Remove AIC and BIC PDFs

* Catching missing species WIP

* Remove unnecessary newick_tree variable

* Improve checking steps for FASTA and latin names.

Exit if latin_names is empty or one or more species are missing.
The new function check_complete_dictionary() lists the missing
species in latin_names and exits.

Check and warn if FASTA of GFF files are missing; exit after all
the files have been checked.

* Update test_pipeline.yml
* Update README.md

* Update doc/source/concept.rst
* Update doc/source/configuration.rst

* Update ksrates/fc_configfile.py

* Update doc/source/configuration.rst
* Update doc/source/paralogs_analyses.rst

* Update ksrates/correct.py
* Update ksrates/fc_rrt_correction.py

* Accept suggestions by reviewer about renaming

* Rename function "decompose_ortholog_ks"
* Rename function to check file content
* Rename function to check complete latin_names

* Removing comment about Nextflow in plot_tree.py

* Rename back to "species of interest" in wgd files

* Mention GFF file in "colinearity" config field

* Move logging message in setup_correction.py

* Rename "colinearity" to "anchors" in LMM filenames

* Change figure title of anchor Ks clustering picture

* Rename to "focal species" in readme

* Fix RST title

* Link to "paralogs analyses" from expert config

* Apply suggestions from code review

* Replace GFF dict with string; improve checkpoints

* Remove unnecessary function argument

Co-authored-by: cesen <cesen@psb.ugent.be>
Co-authored-by: lohausr <56632794+lohausr@users.noreply.github.com>

* Update config.rst: mainly Nextflow config section
* Apply suggestions from code review
* Fix wgdOrtholog dependencies; improve beforeScript
* Suggest threads/memory resources
* Update test_pipeline.yml

Co-authored-by: cesen <cesen@psb.ugent.be>
Co-authored-by: lohausr <56632794+lohausr@users.noreply.github.com>

Add bioRxiv citation and links