Refactor repo (#5)

* refactor components

* add create_readme script

* restore task_readme

* add helper functions

* Remove github actions

.github/PULL_REQUEST_TEMPLATE.md

@@ -7,7 +7,7 @@
 
 - Check the correct box. Does this PR contain:
   - [ ] Breaking changes
-  - [ ] New functionality (new method, new metric, ...)
+  - [ ] New functionality
   - [ ] Major changes
   - [ ] Minor changes
   - [ ] Bug fixes

component_tests/check_method_config.py

@@ -0,0 +1,132 @@
+import yaml
+
+## VIASH START
+meta = {
+    "config" : "foo"
+}
+## VIASH END
+
+
+NAME_MAXLEN = 50
+
+SUMMARY_MAXLEN = 400
+
+DESCRIPTION_MAXLEN = 5000
+
+_MISSING_DOIS = ["vandermaaten2008visualizing", "hosmer2013applied"]
+
+TIME_LABELS = ["lowtime", "midtime", "hightime"]
+MEM_LABELS = ["lowmem", "midmem", "highmem"]
+CPU_LABELS = ["lowcpu", "midcpu", "highcpu"]
+
+def _load_bib():
+    with open(f"{meta['resources_dir']}/library.bib", "r") as file:
+        return file.read()
+
+def check_url(url):
+    import requests
+    from urllib3.util.retry import Retry
+    from requests.adapters import HTTPAdapter
+
+    # configure retry strategy
+    session = requests.Session()
+    retry = Retry(connect=3, backoff_factor=0.5)
+    adapter = HTTPAdapter(max_retries=retry)
+    session.mount('http://', adapter)
+    session.mount('https://', adapter)
+
+    get = session.head(url)
+
+    if get.ok or get.status_code == 429: # 429 rejected, too many requests
+        return True
+    else:
+        return False
+
+def search_ref_bib(reference):
+    import re
+    bib = _load_bib()
+
+    entry_pattern =  r"(@\w+{[^}]*" + reference + r"[^}]*}(.|\n)*?)(?=@)"
+
+    bib_entry = re.search(entry_pattern, bib)
+
+    if bib_entry:
+
+        type_pattern = r"@(.*){" + reference
+        doi_pattern = r"(?=[Dd][Oo][Ii]\s*=\s*{([^,}]+)})"
+
+        entry_type = re.search(type_pattern, bib_entry.group(1))
+
+        if not (entry_type.group(1) == "misc" or reference in _MISSING_DOIS):
+            entry_doi = re.search(doi_pattern, bib_entry.group(1))
+            assert entry_doi.group(1), "doi not found in bibtex reference"
+            url = f"https://doi.org/{entry_doi.group(1)}"
+            assert check_url(url), f"{url} is not reachable, ref= {reference}."
+
+        return True
+
+    else:
+        return False
+
+print("Load config data", flush=True)
+with open(meta["config"], "r") as file:
+    config = yaml.safe_load(file)
+
+print("Check general fields", flush=True)
+assert len(config["functionality"]["name"]) <= NAME_MAXLEN, f"Component id (.functionality.name) should not exceed {NAME_MAXLEN} characters."
+assert "namespace" in config["functionality"] is not None, "namespace not a field or is empty"
+
+print("Check info fields", flush=True)
+info = config['functionality']['info']
+assert "type" in info, "type not an info field"
+info_types = ["method", "control_method"]
+assert info["type"] in info_types , f"got {info['type']} expected one of {info_types}"
+assert "label" in info is not None, "label not an info field or is empty"
+assert "summary" in info is not None, "summary not an info field or is empty"
+assert "FILL IN:" not in info["summary"], "Summary not filled in"
+assert len(info["summary"]) <= SUMMARY_MAXLEN, f"Component id (.functionality.info.summary) should not exceed {SUMMARY_MAXLEN} characters."
+assert "description" in info is not None, "description not an info field or is empty"
+assert "FILL IN:" not in info["description"], "description not filled in"
+assert len(info["description"]) <= DESCRIPTION_MAXLEN, f"Component id (.functionality.info.description) should not exceed {DESCRIPTION_MAXLEN} characters."
+if info["type"] == "method":
+    assert "reference" in info, "reference not an info field"
+    bib = _load_bib()
+    if info["reference"]:
+        reference = info["reference"]
+        if not isinstance(reference, list):
+            reference = [reference]
+        for ref in reference:
+            assert search_ref_bib(ref), f"reference {ref} not added to library.bib"
+    assert "documentation_url" in info is not None, "documentation_url not an info field or is empty"
+    assert "repository_url" in info is not None, "repository_url not an info field or is empty"
+    assert check_url(info["documentation_url"]), f"{info['documentation_url']} is not reachable"
+    assert check_url(info["repository_url"]), f"{info['repository_url']} is not reachable"
+
+if "variants" in info:
+    arg_names = [arg["name"].replace("--", "") for arg in config["functionality"]["arguments"]] + ["preferred_normalization"]
+
+    for paramset_id, paramset in info["variants"].items():
+        if paramset:
+            for arg_id in paramset:
+                assert arg_id in arg_names, f"Argument '{arg_id}' in `.functionality.info.variants['{paramset_id}']` is not an argument in `.functionality.arguments`."
+
+assert "preferred_normalization" in info, "preferred_normalization not an info field"
+norm_methods = ["log_cpm", "log_cp10k", "counts", "log_scran_pooling", "sqrt_cpm", "sqrt_cp10k", "l1_sqrt"]
+assert info["preferred_normalization"] in norm_methods, "info['preferred_normalization'] not one of '" + "', '".join(norm_methods) + "'."
+
+print("Check platform fields", flush=True)
+platforms = config['platforms']
+for platform in platforms:
+    if not platform["type"] == "nextflow":
+        continue
+    nextflow= platform
+
+assert nextflow, "nextflow not a platform"
+assert nextflow["directives"], "directives not a field in nextflow platform"
+assert nextflow["directives"]["label"], "label not a field in nextflow platform directives"
+
+assert [i for i in nextflow["directives"]["label"] if i in TIME_LABELS], "time label not filled in"
+assert [i for i in nextflow["directives"]["label"] if i in MEM_LABELS], "mem label not filled in"
+assert [i for i in nextflow["directives"]["label"] if i in CPU_LABELS], "cpu label not filled in"
+
+print("All checks succeeded!", flush=True)