Keep the linter happy

cbg-ethz · Feb 22, 2024 · a0159ae · a0159ae
1 parent 62b6bf1
commit a0159ae
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Showing 6 changed files with 57 additions and 41 deletions.
diff --git a/cojac/cooc_colourmut.py b/cojac/cooc_colourmut.py
@@ -62,12 +62,14 @@ def cooc_colourmut(amp, json_fname, yaml_fname):
     amplicon_nfo = {
         a: ",".join(
             [
-                f"{p}{b}"
-                if len(b) == 1
-                else (
-                    f"\u0394{p}-{p + len(b) - 1}"
-                    if b == "-" * len(b)
-                    else f"{p}\u2192{b}"
+                (
+                    f"{p}{b}"
+                    if len(b) == 1
+                    else (
+                        f"\u0394{p}-{p + len(b) - 1}"
+                        if b == "-" * len(b)
+                        else f"{p}\u2192{b}"
+                    )
                 )
                 for p, b in aqu[4].items()
             ]

diff --git a/cojac/cooc_curate.py b/cojac/cooc_curate.py
@@ -59,16 +59,18 @@ def getAccessKey():
         return netrc.netrc().authenticators(urlparse(server).netloc)[2]
     except:
         print(
-            f"no access key found for {urlparse(server).netloc} in ~/.netrc\n"
-            f"your requests are likely to be not allowed by the server\n"
-            f"please add the following entry in your ~/.netrc:\n"
-            f"```\n"
-            f"machine {urlparse(server).netloc}\n"
-            f"password <YOUR_ACCESS_KEY_HERE>\n"
-            f"```\n"
-            f"or use the COVSPECTRUM_ACCESSKEY envrionment variable\n"
-            if "open" not in server
-            else f"(not using access keys on API {server})",
+            (
+                f"no access key found for {urlparse(server).netloc} in ~/.netrc\n"
+                f"your requests are likely to be not allowed by the server\n"
+                f"please add the following entry in your ~/.netrc:\n"
+                f"```\n"
+                f"machine {urlparse(server).netloc}\n"
+                f"password <YOUR_ACCESS_KEY_HERE>\n"
+                f"```\n"
+                f"or use the COVSPECTRUM_ACCESSKEY envrionment variable\n"
+                if "open" not in server
+                else f"(not using access keys on API {server})"
+            ),
             file=sys.stderr,
         )
         # sys.exit(1)

diff --git a/cojac/cooc_mutbamscan.py b/cojac/cooc_mutbamscan.py
@@ -103,12 +103,16 @@ def scanamplicon(read_iter, mut_dict):
 
     # look at last column only
     return {
-        "sites": dict(zip(sites_cnt[0].tolist(), sites_cnt[1].tolist()))
-        if len(all_sites)
-        else {},
-        "muts": dict(zip(muts_cnt[0].tolist(), muts_cnt[1].tolist()))
-        if len(all_muts)
-        else {},
+        "sites": (
+            dict(zip(sites_cnt[0].tolist(), sites_cnt[1].tolist()))
+            if len(all_sites)
+            else {}
+        ),
+        "muts": (
+            dict(zip(muts_cnt[0].tolist(), muts_cnt[1].tolist()))
+            if len(all_muts)
+            else {}
+        ),
     }
 
 
@@ -278,9 +282,11 @@ def make_all_amplicons(amp_bed, vocs, revert=False, n_cooc=2):
         loaded_yamls.append(
             filter_decode_vartiant(
                 loaded_yaml,
-                categories=["revert", "mut", "extra", "shared", "subset"]
-                if revert
-                else ["mut", "extra", "shared", "subset"],
+                categories=(
+                    ["revert", "mut", "extra", "shared", "subset"]
+                    if revert
+                    else ["mut", "extra", "shared", "subset"]
+                ),
             )
         )
 
@@ -307,9 +313,9 @@ def make_all_amplicons(amp_bed, vocs, revert=False, n_cooc=2):
                 print(f"{k1} is identical to {k2}")
                 # sort the variant names part of the list, to be consistent between calls, no matter the filesystem's on-disk order
                 # (i.e.: no 76_AY42_IN2 vs 76_IN2_AY42)
-                amplicons[
-                    "_".join([npart[0]] + sorted(npart[1:] + [yam["name"]]))
-                ] = amplicons.pop(k2)
+                amplicons["_".join([npart[0]] + sorted(npart[1:] + [yam["name"]]))] = (
+                    amplicons.pop(k2)
+                )
                 del amp_dict[k1]
                 break
 

diff --git a/cojac/cooc_pubmut.py b/cojac/cooc_pubmut.py
@@ -148,12 +148,14 @@ def cooc_pubmut(
                     # TODO incorporate output of curate
                     ",".join(
                         [
-                            f"{p}{b}"
-                            if len(b) == 1
-                            else (
-                                f"\u0394{p}-{p + len(b) - 1}"
-                                if b == "-" * len(b)
-                                else f"{p}\u2192{b}"
+                            (
+                                f"{p}{b}"
+                                if len(b) == 1
+                                else (
+                                    f"\u0394{p}-{p + len(b) - 1}"
+                                    if b == "-" * len(b)
+                                    else f"{p}\u2192{b}"
+                                )
                             )
                             for p, b in aqu[4].items()
                         ]

diff --git a/cojac/cooc_tabmut.py b/cojac/cooc_tabmut.py
@@ -153,9 +153,11 @@ def cooc_tabmut(
                 line.update(
                     {
                         "amplicon": anum,
-                        "frac": (float(muts_cnt) / float(sites_cnt))
-                        if sites_cnt
-                        else float("nan"),
+                        "frac": (
+                            (float(muts_cnt) / float(sites_cnt))
+                            if sites_cnt
+                            else float("nan")
+                        ),
                         "cooc": (sites_cnt_l if int(sites_cnt_l) > 0 else ""),
                         "count": sites_cnt,
                         "mut_all": muts_cnt,
@@ -171,9 +173,11 @@ def cooc_tabmut(
                         (ampcol, "count"): sites_cnt,
                         (ampcol, "mut_all"): muts_cnt,
                         (ampcol, "mut_oneless"): mut_oneless,
-                        (ampcol, "frac"): (float(muts_cnt) / float(sites_cnt))
-                        if sites_cnt
-                        else float("nan"),
+                        (ampcol, "frac"): (
+                            (float(muts_cnt) / float(sites_cnt))
+                            if sites_cnt
+                            else float("nan")
+                        ),
                         (ampcol, "cooc"): (sites_cnt_l if int(sites_cnt_l) > 0 else ""),
                     }
                 )

diff --git a/pyproject.toml b/pyproject.toml
@@ -27,7 +27,7 @@ click = "^8.0.3"
 requests = "^2.27.1"
 
 [tool.poetry.dev-dependencies]
-black = "^22.1.0"
+black = "^24.2.0"
 pytest = "^6.2.1"
 
 [tool.poetry.scripts]