feat: Add Public init using Kingfisher

.circleci/config.yml

@@ -88,7 +88,7 @@ jobs:
             source activate ./atlasenv
             atlas init --db-dir $DATABASE_DIR --threads 1 --working-dir test/Getenvs test/reads/empty
       - run:
-          name: install environements
+          name: install environments
           command: |
             source activate ./atlasenv
             atlas run all --working-dir test/Getenvs --conda-create-envs-only --cores all

.github/workflows/codespell.yml

@@ -21,7 +21,3 @@ jobs:
         uses: actions/checkout@v4
       - name: Codespell
         uses: codespell-project/actions-codespell@v2
-        with:
-          check_filenames: true
-          skip: ".git,*.pdf,*.svg,versioneer.py,*.css,*.html"
-          check_hidden: true

.github/workflows/python-package-conda.yml

@@ -106,7 +106,7 @@ jobs:
           path: databases
           key: conda-envs-assembly
 
-        # - name: upack conda envs
+        # - name: unpack conda envs
         #   if: steps.get-envs.outputs.cache-hit != 'true'
         #   run: tar -xzf assembly_conda_envs.tar.gz
 
@@ -198,7 +198,7 @@ jobs:
           path: wd
           key: assembly-working-dir
 
-      - name: dryrun assembly shold need nothing to be done
+      - name: dryrun assembly should need nothing to be done
         run: |
           ls -l wd
           ls -l databases/conda_envs
@@ -264,7 +264,7 @@ jobs:
           fail-on-cache-miss: true
           key: assembly-working-dir
 
-      - name: dryrun assembly shold need nothing to be done
+      - name: dryrun assembly should need nothing to be done
         run: |
           ls -l wd
           ls -l databases

CHANGELOG.md

@@ -20,12 +20,12 @@ Fix error with downloading DRAM. Update to DRAM v1.5
 
 - Qc reads, assembly are now written in the sample.tsv from the start. This should fix errors of partial writing to the sample.tsv https://github.com/metagenome-atlas/atlas/issues/695
 - It also allows you to add external assemblies.
-- singletons reads are no longer used trough the pipeline. 
+- singletons reads are no longer used through the pipeline. 
 - This changes the default paths for raw reads and assemblies. 
 assembly are now in `Assembly/fasta/{sample}.fasta`
 reads: `QC/reads/{sample}_{fraction}.fastq.gz`
 
-**Seemless update**: If you update atlas and continue on an old project. Your old files will be copied.
+**Seamless update**: If you update atlas and continue on an old project. Your old files will be copied.
 Or the path defined in the sample.tsv will be used. 
 
 

CONTRIBUTING.md

@@ -24,7 +24,7 @@ I hope we can help you...
 
 You can ask the maintainers to be added to the repository and work from a *branch* of the main atlas repository or you can work from a fork of the atlas repository. 
 
-Follow the [steps](https://github.com/metagenome-atlas/atlas#install-the-development-version-from-github) to set up the developpment version of atlas. This allows you to work with the code you have in the git repository. 
+Follow the [steps](https://github.com/metagenome-atlas/atlas#install-the-development-version-from-github) to set up the development version of atlas. This allows you to work with the code you have in the git repository. 
 
 ## Test the code
 ### Locally
@@ -36,8 +36,8 @@ When you created a new rule and you want to test the output of this rule `my_tar
 
 
 
-### Continous integration
-When you make a pull request to the master branch. Each change in your code get's checked by continous integration (CI). The tests should make shure that your modification don't break any other use of atlas. However due to the requeirements needed during the execution of atlas, it is not possible to test all functionalities via CI. If you add functionalities to atlas, they should also be tested. Have a look at the scripts in `.test`.
+### Continuous integration
+When you make a pull request to the master branch. Each change in your code gets checked by continuous integration (CI). The tests should make sure that your modification don't break any other use of atlas. However due to the requeirements needed during the execution of atlas, it is not possible to test all functionalities via CI. If you add functionalities to atlas, they should also be tested. Have a look at the scripts in `.test`.
 
 
 

README.md

@@ -38,7 +38,7 @@ https://metagenome-atlas.readthedocs.io/
 > doi: [10.1186/s12859-020-03585-4](https://doi.org/10.1186/s12859-020-03585-4)
 
 
-# Developpment/Extensions
+# Development/Extensions
 
 Here are some ideas I work or want to work on when I have time. If you want to contribute or have some ideas let me know via a feature request issue.
 

atlas/atlas.py

@@ -9,7 +9,7 @@
 
 from snakemake.io import load_configfile
 from .make_config import validate_config
-from .init.atlas_init import run_init  # , run_init_sra
+from .init.atlas_init import run_init, run_init_sra
 
 from .__init__ import __version__
 
@@ -32,7 +32,7 @@ def handle_max_mem(max_mem, profile):
         import psutil
         from math import floor
 
-        # calulate max  system meory in GB (float!)
+        # calculate max  system memory in GB (float!)
         max_system_memory = psutil.virtual_memory().total / (1024**3)
 
         if max_mem is None:
@@ -66,7 +66,7 @@ def cli(obj):
 cli.add_command(run_init)
 
 
-# cli.add_command(run_init_sra)
+cli.add_command(run_init_sra)
 
 
 def get_snakefile(file="workflow/Snakefile"):
@@ -146,7 +146,7 @@ def get_snakefile(file="workflow/Snakefile"):
 def run_workflow(
     workflow, working_dir, config_file, jobs, max_mem, profile, dryrun, snakemake_args
 ):
-    """Runs the ATLAS pipline
+    """Runs the ATLAS pipeline
 
     By default all steps are executed but a sub-workflow can be specified.
     Needs a config-file and expects to find a sample table in the working-directory. Both can be generated with 'atlas init'