seqtree 0.6.0__tar.gz → 0.6.1__tar.gz

{seqtree-0.6.0 → seqtree-0.6.1}/CHANGELOG.md

@@ -3,6 +3,17 @@
 All notable changes to `seqtree`. Dates are release dates; the project is pre-1.0, so a **minor**
 bump may carry breaking changes.
 
+## [0.6.1] — 2026-07-30
+
+### Fixed
+
+- **`gapblock_matrix`'s out-of-alphabet error named only the bad symbol**, not which sequence it
+  came from (`"symbol '_' is not in the alphabet"`) — unhelpful when a single malformed row (e.g.
+  a `junction_aa` containing a legacy out-of-frame marker) is buried in a batch of hundreds of
+  thousands. The message now names the side, index, and offending string:
+  `"queries[42] ('CASSIRS_YEQYF'): symbol '_' is not in the alphabet"`. No change to which symbols
+  are accepted (still the standard 20 + B/Z/X/* for `alphabet="aa"`).
+
 ## [0.6.0] — 2026-07-17
 
 ### Fixed

{seqtree-0.6.0 → seqtree-0.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: seqtree
-Version: 0.6.0
+Version: 0.6.1
 Summary: Fast fuzzy search over biological sequences (C++ core, Python bindings)
 Keywords: sequence-search,fuzzy-matching,CDR3,immunology,bioinformatics,trie
 Author-Email: ISALGO laboratory <mikhail.shugay@gmail.com>
@@ -114,8 +114,11 @@ needs a C++17 compiler and CMake (pulled in automatically by the build).
 
 ## Build from source
 
+Needs [uv](https://docs.astral.sh/uv/) (`brew install uv`); `setup.sh` uses it for the venv and
+the editable install.
+
 ```fish
-bash setup.sh            # repo-local .venv + editable install
+bash setup.sh            # uv-managed .venv + editable install
 bash setup.sh --tests    # + pytest
 bash setup.sh --bench     # + benchmark deps (huggingface_hub, psutil)
 ```

{seqtree-0.6.0 → seqtree-0.6.1}/README.md

@@ -80,8 +80,11 @@ needs a C++17 compiler and CMake (pulled in automatically by the build).
 
 ## Build from source
 
+Needs [uv](https://docs.astral.sh/uv/) (`brew install uv`); `setup.sh` uses it for the venv and
+the editable install.
+
 ```fish
-bash setup.sh            # repo-local .venv + editable install
+bash setup.sh            # uv-managed .venv + editable install
 bash setup.sh --tests    # + pytest
 bash setup.sh --bench     # + benchmark deps (huggingface_hub, psutil)
 ```

{seqtree-0.6.0 → seqtree-0.6.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "seqtree"
-version = "0.6.0"
+version = "0.6.1"
 description = "Fast fuzzy search over biological sequences (C++ core, Python bindings)"
 readme = "README.md"
 requires-python = ">=3.10"

{seqtree-0.6.0 → seqtree-0.6.1}/skills/seqtree/SKILL.md

@@ -237,7 +237,7 @@ Count it in the control.
 4. OLGA generates from `P_gen`, which is **not** the post-selection background `P_0`. Do not use
    an OLGA sample as the null for an operational cutoff.
 5. Rebuild after pulling: a stale `_core.so` has silently shadowed new Python-visible C++ methods
-   more than once (`pip install -e .`).
+   more than once (`bash setup.sh`, or `uv pip install -e .`).
 
 ## Layering
 

{seqtree-0.6.0 → seqtree-0.6.1}/src/gapblock.cpp

@@ -9,13 +9,13 @@
 namespace seqtree {
 namespace {
 
-std::vector<uint8_t> encode(const Codec& c, const std::string& s) {
+std::vector<uint8_t> encode(const Codec& c, const std::string& s, const char* label, size_t idx) {
     std::vector<uint8_t> out(s.size());
     for (size_t i = 0; i < s.size(); ++i) {
         uint8_t v = c.encode(s[i]);
         if (v == Codec::kInvalid)
-            throw std::invalid_argument(std::string("symbol '") + s[i] +
-                                        "' is not in the alphabet");
+            throw std::invalid_argument(label + std::string("[") + std::to_string(idx) + "] ('" + s +
+                                        "'): symbol '" + s[i] + "' is not in the alphabet");
         out[i] = v;
     }
     return out;
@@ -85,11 +85,11 @@ std::vector<int32_t> gapblock_matrix(const std::vector<std::string>& queries,
     std::vector<std::vector<uint8_t>> qc(N), rc(K);
     uint32_t longest = 0;
     for (size_t i = 0; i < N; ++i) {
-        qc[i] = encode(codec, queries[i]);
+        qc[i] = encode(codec, queries[i], "queries", i);
         longest = std::max<uint32_t>(longest, uint32_t(qc[i].size()));
     }
     for (size_t k = 0; k < K; ++k) {
-        rc[k] = encode(codec, refs[k]);
+        rc[k] = encode(codec, refs[k], "refs", k);
         longest = std::max<uint32_t>(longest, uint32_t(rc[k].size()));
     }