leave Python changes for another PR

.github/workflows/codspeed.yml

@@ -32,22 +32,3 @@ jobs:
         with:
           run: "cd src/core && cargo codspeed run"
           token: ${{ secrets.CODSPEED_TOKEN }}
-
-  benchmarks-python:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v3
-        with:
-          python-version: "3.12"
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install tox
-
-      - name: Run benchmarks
-        uses: CodSpeedHQ/action@v2
-        with:
-          token: ${{ secrets.CODSPEED_TOKEN }}
-          run: tox -e codspeed

.github/workflows/rust.yml

@@ -260,7 +260,7 @@ jobs:
         uses: actions-rs/cargo@v1
         with:
           command: build
-          args: --all-features --tests
+          args: --all-features
 
   check_cbindgen:
     name: "Check if cbindgen runs cleanly for generating the C headers"

benchmarks/benchmarks.py

@@ -33,6 +33,74 @@ def load_sequences():
     return sequences
 
 
+class TimeMinHashSuite:
+    def setup(self):
+        self.mh = MinHash(MINHASH_NUM, MINHASH_K, track_abundance=False)
+        self.protein_mh = MinHash(
+            MINHASH_NUM, MINHASH_K, is_protein=True, track_abundance=False
+        )
+        self.sequences = load_sequences()
+
+        self.populated_mh = MinHash(MINHASH_NUM, MINHASH_K, track_abundance=False)
+        for seq in self.sequences:
+            self.populated_mh.add_sequence(seq)
+
+    def time_add_sequence(self):
+        mh = self.mh
+        sequences = self.sequences
+        for seq in sequences:
+            mh.add_sequence(seq)
+
+    def time_add_protein(self):
+        mh = self.protein_mh
+        sequences = self.sequences
+        for seq in sequences:
+            mh.add_protein(seq)
+
+    def time_get_mins(self):
+        mh = self.populated_mh
+        for i in range(GET_MINS_RANGE):
+            mh.get_mins()
+
+    def time_add_hash(self):
+        mh = self.mh
+        for i in range(ADD_HASH_RANGE):
+            mh.add_hash(i)
+
+    def time_add_many(self):
+        mh = self.mh
+        mh.add_many(list(range(ADD_MANY_RANGE)))
+
+    def time_similarity(self):
+        mh = self.mh
+        other_mh = self.populated_mh
+        for i in range(SIMILARITY_TIMES):
+            mh.similarity(other_mh)
+
+    def time_count_common(self):
+        mh = self.mh
+        other_mh = self.populated_mh
+        for i in range(COUNT_COMMON_TIMES):
+            mh.count_common(other_mh)
+
+    def time_merge(self):
+        mh = self.mh
+        other_mh = self.populated_mh
+        for i in range(MERGE_TIMES):
+            mh.merge(other_mh)
+
+    def time_copy(self):
+        mh = self.populated_mh
+        for i in range(COPY_TIMES):
+            mh.__copy__()
+
+    def time_concat(self):
+        mh = self.mh
+        other_mh = self.populated_mh
+        for i in range(CONCAT_TIMES):
+            mh += other_mh
+
+
 class PeakmemMinHashSuite:
     def setup(self):
         self.mh = MinHash(MINHASH_NUM, MINHASH_K, track_abundance=True)
@@ -66,6 +134,33 @@ def peakmem_add_many(self):
 ####################
 
 
+class TimeMinAbundanceSuite(TimeMinHashSuite):
+    def setup(self):
+        TimeMinHashSuite.setup(self)
+        self.mh = MinHash(MINHASH_NUM, MINHASH_K, track_abundance=True)
+
+        self.populated_mh = MinHash(MINHASH_NUM, MINHASH_K, track_abundance=True)
+        for seq in self.sequences:
+            self.populated_mh.add_sequence(seq)
+
+    def time_get_mins_abundance(self):
+        mh = self.populated_mh
+        for i in range(GET_MINS_RANGE):
+            mh.get_mins(with_abundance=True)
+
+    def time_set_abundances(self):
+        mh = self.mh
+        mins = self.populated_mh.get_mins(with_abundance=True)
+        for i in range(SET_ABUNDANCES_RANGE):
+            mh.set_abundances(mins)
+
+    def time_set_abundances_noclear(self):
+        mh = self.mh
+        mins = self.populated_mh.get_mins(with_abundance=True)
+        for i in range(SET_ABUNDANCES_RANGE):
+            mh.set_abundances(mins, clear=False)
+
+
 class PeakmemMinAbundanceSuite(PeakmemMinHashSuite):
     def setup(self):
         PeakmemMinHashSuite.setup(self)
@@ -75,6 +170,35 @@ def setup(self):
 ####################
 
 
+class TimeZipStorageSuite:
+    def setup(self):
+        import zipfile
+
+        self.zipfile = NamedTemporaryFile()
+
+        with zipfile.ZipFile(
+            self.zipfile, mode="w", compression=zipfile.ZIP_STORED
+        ) as storage:
+            for i in range(ZIP_STORAGE_WRITE):
+                # just so we have lots of entries
+                storage.writestr(str(i), b"0")
+            # one big-ish entry
+            storage.writestr("sig1", b"9" * 1_000_000)
+
+    def time_load_from_zipstorage(self):
+        with ZipStorage(self.zipfile.name) as storage:
+            for i in range(ZIP_STORAGE_LOAD):
+                storage.load("sig1")
+
+    def time_load_small_from_zipstorage(self):
+        with ZipStorage(self.zipfile.name) as storage:
+            for i in range(ZIP_STORAGE_LOAD):
+                storage.load("99999")
+
+    def teardown(self):
+        self.zipfile.close()
+
+
 class PeakmemZipStorageSuite:
     def setup(self):
         import zipfile

pyproject.toml

@@ -103,7 +103,6 @@ test = [
   "pytest>=6.2.4,<8.4.0",
   "pytest-cov>=4,<6.0",
   "pytest-xdist>=3.1",
-  "pytest-benchmark>=4.0",
   "pyyaml>=6,<7",
   "diff-cover>=7.3",
   "covdefaults>=2.2.2",