chore: update version for release of v0.1.0

CHANGELOG.md

@@ -1,4 +1,63 @@
-## Tools development version
+## Tools 0.1.0
+
+The Tools repository is now restructured as a Python package.
+All previous python scripts which included command line utilities have been
+moved to `src/`, and all other scripts have been moved to `scripts/`.
+In both cases, they are available in the path when the package is installed.
+
+Functions which were part of both XAVIER and RENEE are available for re-use in
+other bioinformatics pipelines for tasks such as determining the HPC
+environment, retrieving available genome annotations, and printing citation and
+version information.
+Explore the `ccbr_tools` reference documentation for more information:
+<https://ccbr.github.io/Tools/latest/reference/>
+
+### CLI Utilities
+
+Command-line utilities in CCBR Tools.
+
+- `ccbr_tools`
+- `gb2gtf`
+- `hf`
+- `intersect`
+- `jobby`
+- `jobinfo`
+- `peek`
+
+Run a command with `--help` to learn how to use it.
+
+### External Scripts
+
+Additional standalone scripts for various common tasks in
+[scripts/](scripts/) are added to the path when this package is
+installed. They are less robust than the CLI Utilities included in the
+package and do not have any unit tests.
+
+- `add_gene_name_to_count_matrix.R`
+- `aggregate_data_tables.R`
+- `argparse.bash`
+- `cancel_snakemake_jobs.sh`
+- `create_hpc_link.sh`
+- `extract_value_from_json.py`
+- `extract_value_from_yaml.py`
+- `filter_bam_by_readids.py`
+- `filter_fastq_by_readids_highmem.py`
+- `filter_fastq_by_readids_highmem_pe.py`
+- `gather_cluster_stats.sh`
+- `gather_cluster_stats_biowulf.sh`
+- `get_buyin_partition_list.bash`
+- `get_slurm_file_with_error.sh`
+- `gsea_preranked.sh`
+- `karyoploter.R`
+- `make_labels_for_pipeliner.sh`
+- `rawcounts2normalizedcounts_DESeq2.R`
+- `rawcounts2normalizedcounts_limmavoom.R`
+- `run_jobby_on_nextflow_log`
+- `run_jobby_on_nextflow_log_full_format`
+- `run_jobby_on_snakemake_log`
+- `run_jobby_on_snakemake_log_full_format`
+- `spooker`
+- `which_vpn.sh`
 
 ## Tools 0.0.1
 

VERSION

@@ -0,0 +1 @@
+src/ccbr_tools/VERSION

src/ccbr_tools/VERSION

@@ -1 +1 @@
-0.1.0-dev
+0.1.0