[pre-commit.ci] pre-commit autoupdate (#3290)

updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.6 → v0.5.7](astral-sh/ruff-pre-commit@v0.5.6...v0.5.7)  Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
sourmash-bio · Aug 20, 2024 · d3ae5da · d3ae5da
1 parent 38edd5b
commit d3ae5da
Show file tree

Hide file tree

Showing 5 changed files with 134 additions and 94 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -10,7 +10,7 @@ repos:
       - id: check-toml
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.6
+    rev: v0.6.1
     hooks:
       - id: ruff-format
       - id: ruff

diff --git a/doc/kmers-and-minhash.ipynb b/doc/kmers-and-minhash.ipynb
@@ -49,10 +49,10 @@
     "def jaccard_similarity(a, b):\n",
     "    a = set(a)\n",
     "    b = set(b)\n",
-    "    \n",
+    "\n",
     "    intersection = len(a.intersection(b))\n",
     "    union = len(a.union(b))\n",
-    "    \n",
+    "\n",
     "    return intersection / union"
    ]
   },
@@ -65,9 +65,9 @@
     "def jaccard_containment(a, b):\n",
     "    a = set(a)\n",
     "    b = set(b)\n",
-    "    \n",
+    "\n",
     "    intersection = len(a.intersection(b))\n",
-    "    \n",
+    "\n",
     "    return intersection / len(a)"
    ]
   },
@@ -84,9 +84,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "a = ['ATGG', 'AACC']\n",
-    "b = ['ATGG', 'CACA']\n",
-    "c = ['ATGC', 'CACA']"
+    "a = [\"ATGG\", \"AACC\"]\n",
+    "b = [\"ATGG\", \"CACA\"]\n",
+    "c = [\"ATGC\", \"CACA\"]"
    ]
   },
   {
@@ -270,11 +270,11 @@
     "def build_kmers(sequence, ksize):\n",
     "    kmers = []\n",
     "    n_kmers = len(sequence) - ksize + 1\n",
-    "    \n",
+    "\n",
     "    for i in range(n_kmers):\n",
-    "        kmer = sequence[i:i + ksize]\n",
+    "        kmer = sequence[i : i + ksize]\n",
     "        kmers.append(kmer)\n",
-    "        \n",
+    "\n",
     "    return kmers"
    ]
   },
@@ -307,7 +307,7 @@
     }
    ],
    "source": [
-    "build_kmers('ATGGACCAGATATAGGGAGAGCCAGGTAGGACA', 21)"
+    "build_kmers(\"ATGGACCAGATATAGGGAGAGCCAGGTAGGACA\", 21)"
    ]
   },
   {
@@ -325,8 +325,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "seq1 = 'ATGGACCAGATATAGGGAGAGCCAGGTAGGACA'\n",
-    "seq2 = 'ATGGACCAGATATTGGGAGAGCCGGGTAGGACA'\n",
+    "seq1 = \"ATGGACCAGATATAGGGAGAGCCAGGTAGGACA\"\n",
+    "seq2 = \"ATGGACCAGATATTGGGAGAGCCGGGTAGGACA\"\n",
     "# differences:       ^         ^"
    ]
   },
@@ -375,13 +375,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import screed # a library for reading in FASTA/FASTQ\n",
+    "import screed  # a library for reading in FASTA/FASTQ\n",
+    "\n",
     "\n",
     "def read_kmers_from_file(filename, ksize):\n",
     "    all_kmers = []\n",
     "    for record in screed.open(filename):\n",
     "        sequence = record.sequence\n",
-    "        \n",
+    "\n",
     "        kmers = build_kmers(sequence, ksize)\n",
     "        all_kmers += kmers\n",
     "\n",
@@ -394,7 +395,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "akker_kmers = read_kmers_from_file('genomes/akkermansia.fa', 31)"
+    "akker_kmers = read_kmers_from_file(\"genomes/akkermansia.fa\", 31)"
    ]
   },
   {
@@ -444,8 +445,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "shew1_kmers = read_kmers_from_file('genomes/shew_os185.fa', 31)\n",
-    "shew2_kmers = read_kmers_from_file('genomes/shew_os223.fa', 31)"
+    "shew1_kmers = read_kmers_from_file(\"genomes/shew_os185.fa\", 31)\n",
+    "shew2_kmers = read_kmers_from_file(\"genomes/shew_os223.fa\", 31)"
    ]
   },
   {
@@ -471,9 +472,9 @@
     }
    ],
    "source": [
-    "print('akker vs shew1', jaccard_similarity(akker_kmers, shew1_kmers))\n",
-    "print('akker vs shew2', jaccard_similarity(akker_kmers, shew2_kmers))\n",
-    "print('shew1 vs shew2', jaccard_similarity(shew1_kmers, shew2_kmers))"
+    "print(\"akker vs shew1\", jaccard_similarity(akker_kmers, shew1_kmers))\n",
+    "print(\"akker vs shew2\", jaccard_similarity(akker_kmers, shew2_kmers))\n",
+    "print(\"shew1 vs shew2\", jaccard_similarity(shew1_kmers, shew2_kmers))"
    ]
   },
   {
@@ -492,9 +493,9 @@
     }
    ],
    "source": [
-    "print('akker vs shew1', jaccard_containment(akker_kmers, shew1_kmers))\n",
-    "print('akker vs shew2', jaccard_containment(akker_kmers, shew2_kmers))\n",
-    "print('shew1 vs shew2', jaccard_containment(shew1_kmers, shew2_kmers))"
+    "print(\"akker vs shew1\", jaccard_containment(akker_kmers, shew1_kmers))\n",
+    "print(\"akker vs shew2\", jaccard_containment(akker_kmers, shew2_kmers))\n",
+    "print(\"shew1 vs shew2\", jaccard_containment(shew1_kmers, shew2_kmers))"
    ]
   },
   {
@@ -568,20 +569,22 @@
    "source": [
     "import mmh3\n",
     "\n",
+    "\n",
     "def hash_kmer(kmer):\n",
     "    # calculate the reverse complement\n",
     "    rc_kmer = screed.rc(kmer)\n",
-    "    \n",
+    "\n",
     "    # determine whether original k-mer or reverse complement is lesser\n",
     "    if kmer < rc_kmer:\n",
     "        canonical_kmer = kmer\n",
     "    else:\n",
     "        canonical_kmer = rc_kmer\n",
-    "        \n",
+    "\n",
     "    # calculate murmurhash using a hash seed of 42\n",
     "    hash = mmh3.hash64(canonical_kmer, 42)[0]\n",
-    "    if hash < 0: hash += 2**64\n",
-    "        \n",
+    "    if hash < 0:\n",
+    "        hash += 2**64\n",
+    "\n",
     "    # done\n",
     "    return hash"
    ]
@@ -610,7 +613,7 @@
     }
    ],
    "source": [
-    "hash_kmer('ATGGC')"
+    "hash_kmer(\"ATGGC\")"
    ]
   },
   {
@@ -637,7 +640,7 @@
     }
    ],
    "source": [
-    "hash_kmer('ATGGC')"
+    "hash_kmer(\"ATGGC\")"
    ]
   },
   {
@@ -664,7 +667,7 @@
     }
    ],
    "source": [
-    "hash_kmer('GCCAT')"
+    "hash_kmer(\"GCCAT\")"
    ]
   },
   {
@@ -691,7 +694,7 @@
     }
    ],
    "source": [
-    "hash_kmer('GCCAA')"
+    "hash_kmer(\"GCCAA\")"
    ]
   },
   {
@@ -836,7 +839,7 @@
     "        if hash_kmer(kmer) < keep_below:\n",
     "            keep.append(kmer)\n",
     "        # otherwise, discard\n",
-    "        \n",
+    "\n",
     "    return keep"
    ]
   },
@@ -901,8 +904,8 @@
     }
    ],
    "source": [
-    "print('akker vs akker, total', jaccard_similarity(akker_kmers, akker_kmers))\n",
-    "print('akker vs akker, sub', jaccard_similarity(akker_sub, akker_sub))"
+    "print(\"akker vs akker, total\", jaccard_similarity(akker_kmers, akker_kmers))\n",
+    "print(\"akker vs akker, sub\", jaccard_similarity(akker_sub, akker_sub))"
    ]
   },
   {
@@ -920,8 +923,8 @@
     }
    ],
    "source": [
-    "print('akker vs shew1, total', jaccard_similarity(akker_kmers, shew1_kmers))\n",
-    "print('akker vs shew1, sub', jaccard_similarity(akker_sub, shew1_sub))"
+    "print(\"akker vs shew1, total\", jaccard_similarity(akker_kmers, shew1_kmers))\n",
+    "print(\"akker vs shew1, sub\", jaccard_similarity(akker_sub, shew1_sub))"
    ]
   },
   {
@@ -939,8 +942,8 @@
     }
    ],
    "source": [
-    "print('shew1 vs shew2, total', jaccard_similarity(shew1_kmers, shew2_kmers))\n",
-    "print('shew1 vs shew2, sub', jaccard_similarity(shew1_sub, shew2_sub))"
+    "print(\"shew1 vs shew2, total\", jaccard_similarity(shew1_kmers, shew2_kmers))\n",
+    "print(\"shew1 vs shew2, sub\", jaccard_similarity(shew1_sub, shew2_sub))"
    ]
   },
   {

diff --git a/doc/plotting-compare.ipynb b/doc/plotting-compare.ipynb
@@ -107,7 +107,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "matrix, labels = fig.load_matrix_and_labels('compare-demo')"
+    "matrix, labels = fig.load_matrix_and_labels(\"compare-demo\")"
    ]
   },
   {
@@ -139,8 +139,8 @@
     }
    ],
    "source": [
-    "print('matrix:\\n', matrix)\n",
-    "print('labels:', labels)"
+    "print(\"matrix:\\n\", matrix)\n",
+    "print(\"labels:\", labels)"
    ]
   },
   {
@@ -192,8 +192,8 @@
     }
    ],
    "source": [
-    "print('reordered matrix:\\n', reordered_matrix)\n",
-    "print('reordered labels:', reordered_labels)"
+    "print(\"reordered matrix:\\n\", reordered_matrix)\n",
+    "print(\"reordered labels:\", reordered_labels)"
    ]
   },
   {
@@ -218,8 +218,10 @@
    "source": [
     "import scipy.cluster.hierarchy as sch\n",
     "\n",
-    "def plot_composite_matrix(D, labeltext, show_labels=True,\n",
-    "                          vmax=1.0, vmin=0.0, force=False):\n",
+    "\n",
+    "def plot_composite_matrix(\n",
+    "    D, labeltext, show_labels=True, vmax=1.0, vmin=0.0, force=False\n",
+    "):\n",
     "    \"\"\"Build a composite plot showing dendrogram + distance matrix/heatmap.\n",
     "\n",
     "    Returns a matplotlib figure.\n",
@@ -228,25 +230,34 @@
     "    shown on the plot.\n",
     "    \"\"\"\n",
     "    if D.max() > 1.0 or D.min() < 0.0:\n",
-    "        error('This matrix doesn\\'t look like a distance matrix - min value {}, max value {}', D.min(), D.max())\n",
+    "        error(\n",
+    "            \"This matrix doesn't look like a distance matrix - min value {}, max value {}\",\n",
+    "            D.min(),\n",
+    "            D.max(),\n",
+    "        )\n",
     "        if not force:\n",
     "            raise ValueError(\"not a distance matrix\")\n",
     "        else:\n",
-    "            notify('force is set; scaling to [0, 1]')\n",
+    "            notify(\"force is set; scaling to [0, 1]\")\n",
     "            D -= D.min()\n",
     "            D /= D.max()\n",
     "\n",
     "    if show_labels:\n",
-    "        show_indices = True\n",
+    "        pass\n",
     "\n",
     "    fig = pylab.figure(figsize=(11, 8))\n",
     "    ax1 = fig.add_axes([0.09, 0.1, 0.2, 0.6])\n",
     "\n",
     "    # plot dendrogram\n",
-    "    Y = sch.linkage(D, method='single')  # centroid\n",
+    "    Y = sch.linkage(D, method=\"single\")  # centroid\n",
     "\n",
-    "    Z1 = sch.dendrogram(Y, orientation='left', labels=labeltext,\n",
-    "                        no_labels=not show_labels, get_leaves=True)\n",
+    "    Z1 = sch.dendrogram(\n",
+    "        Y,\n",
+    "        orientation=\"left\",\n",
+    "        labels=labeltext,\n",
+    "        no_labels=not show_labels,\n",
+    "        get_leaves=True,\n",
+    "    )\n",
     "    ax1.set_xticks([])\n",
     "\n",
     "    xstart = 0.45\n",
@@ -256,8 +267,8 @@
     "    scale_xstart = xstart + width + 0.01\n",
     "\n",
     "    # re-order labels along rows, top to bottom\n",
-    "    idx1 = Z1['leaves']\n",
-    "    reordered_labels = [ labeltext[i] for i in idx1 ]\n",
+    "    idx1 = Z1[\"leaves\"]\n",
+    "    reordered_labels = [labeltext[i] for i in idx1]\n",
     "\n",
     "    # reorder D by the clustering in the dendrogram\n",
     "    D = D[idx1, :]\n",
@@ -266,8 +277,9 @@
     "    # show matrix\n",
     "    axmatrix = fig.add_axes([xstart, 0.1, width, 0.6])\n",
     "\n",
-    "    im = axmatrix.matshow(D, aspect='auto', origin='lower',\n",
-    "                          cmap=pylab.cm.YlGnBu, vmin=vmin, vmax=vmax)\n",
+    "    im = axmatrix.matshow(\n",
+    "        D, aspect=\"auto\", origin=\"lower\", cmap=pylab.cm.YlGnBu, vmin=vmin, vmax=vmax\n",
+    "    )\n",
     "    axmatrix.set_xticks([])\n",
     "    axmatrix.set_yticks([])\n",
     "\n",

diff --git a/doc/sourmash-collections.ipynb b/doc/sourmash-collections.ipynb
@@ -405,7 +405,8 @@
    ],
    "source": [
     "from IPython.display import Image\n",
-    "Image(filename='compare_all.mat.matrix.png') "
+    "\n",
+    "Image(filename=\"compare_all.mat.matrix.png\")"
    ]
   },
   {
@@ -857,7 +858,8 @@
    ],
    "source": [
     "import pandas\n",
-    "df = pandas.read_csv('podar-lineage.csv')\n",
+    "\n",
+    "df = pandas.read_csv(\"podar-lineage.csv\")\n",
     "df"
    ]
   },