calkit-python 0.47.2__py3-none-any.whl → 0.47.3__py3-none-any.whl

calkit/cli/latex.py

@@ -5,6 +5,7 @@ from __future__ import annotations
 import hashlib
 import json
 import os
+import re
 import shutil
 import string
 import subprocess
@@ -539,8 +540,44 @@ def _build_diff(
     try:
         # --flatten pulls \input and \include files into one document on
         # each side, so a multi-file paper compares as a whole
+        latexdiff_cmd = ["latexdiff", "--flatten", "--encoding=utf8"]
+        # latexdiff dies trying to open a verbatim input that's a macro
+        # parameter, e.g., \verbatiminput{#1.wcsum} in a \newcommand, so a
+        # filter breaks the line after the command, which TeX reads the same
+        # but latexdiff's pattern doesn't match
+        verbatim_param = re.compile(
+            r"\\(?:verbatiminput\*?|lstinputlisting)"
+            r"\s*(?:\[[^\]\n]*\])?\s*\{[^}\n]*#[0-9]"
+        )
+        sources = [base_tex, head_tex] + [
+            path
+            for side in (base_tex, head_tex)
+            for path in calkit.latex.detect_inputs(side)
+            if Path(path).suffix in calkit.latex._SOURCE_EXTS
+        ]
+        if any(
+            os.path.isfile(path)
+            and verbatim_param.search(
+                Path(path).read_text(encoding="utf-8", errors="replace")
+            )
+            for path in sources
+        ):
+            filter_path = Path(DIFF_TMP_DIR, "verbatim-param-filter.pl")
+            os.makedirs(filter_path.parent, exist_ok=True)
+            # latexdiff appends a newline to what it sends, so drop it
+            filter_path.write_text(
+                "local $/;\n"
+                "my $text = <STDIN>;\n"
+                "$text =~ s/\\n\\z//;\n"
+                "$text =~ s/(\\\\(?:verbatiminput\\*?|lstinputlisting))"
+                "(?=\\s*(?:\\[[^\\]\\n]*\\])?\\s*\\{[^}\\n]*#[0-9])/$1%\\n/g;\n"
+                "print $text;\n"
+            )
+            latexdiff_cmd.append(
+                f"--filter-script=perl {filter_path.as_posix()}"
+            )
         cmd = _tex_cmd(
-            ["latexdiff", "--flatten", "--encoding=utf8", base_tex, head_tex],
+            latexdiff_cmd + [base_tex, head_tex],
             environment=environment,
             no_check=no_check,
             verbose=verbose,

calkit/cli/main/core.py

@@ -1672,6 +1672,14 @@ def push(
             git_cmd = ["git", "push"]
             if not no_recursive and "--recurse-submodules" not in git_args:
                 git_cmd.append("--recurse-submodules=on-demand")
+            # A plain `git push` leaves tags behind, so annotated tags end
+            # up only on the machine that made them
+            if not {
+                "--follow-tags",
+                "--no-follow-tags",
+                "--tags",
+            }.intersection(git_args):
+                git_cmd.append("--follow-tags")
             subprocess.check_call(git_cmd + git_args)
         except subprocess.CalledProcessError:
             raise_error("Git push failed")

calkit/conda.py

@@ -207,6 +207,42 @@ def _normalize_git_dep_url(dep: str) -> str:
     return url.rstrip("/")
 
 
+def _unparseable_version_satisfies(
+    req_spec: str, actual_vers: str
+) -> bool | None:
+    """Check a requirement spec against a version string PEP 440 rejects.
+
+    Returns ``True`` or ``False`` when every clause in ``req_spec`` is a plain
+    equality or inequality (``==``, ``===`` or ``!=``), since those can be
+    decided by comparing the version strings directly. Returns ``None`` when
+    the spec needs version ordering (``<``, ``<=``, ``>``, ``>=``, ``~=``) or
+    contains a wildcard, both of which need a parsed version.
+
+    An empty spec means any version satisfies the requirement.
+
+    The comparison is an exact string match: without a parsed version there is
+    no zero-padding, so ``==1.0`` will not match an installed ``1.0.0``.
+    """
+    if not req_spec:
+        return True
+    clauses = [clause for clause in req_spec.split(",") if clause]
+    for clause in clauses:
+        for op in ("===", "==", "!="):
+            if not clause.startswith(op):
+                continue
+            value = clause[len(op) :]
+            if "*" in value:
+                # Wildcards need normalised versions to expand.
+                return None
+            if (actual_vers == value) == (op == "!="):
+                return False
+            break
+        else:
+            # An ordering operator, or something unrecognized.
+            return None
+    return True
+
+
 def _check_single(
     req: str, actual: str, env_spec_dir: str, conda: bool = False
 ) -> bool:
@@ -248,7 +284,10 @@ def _check_single(
         return _pkg_name_from_dep(req) == _pkg_name_from_dep(actual)
     if req_is_git:
         req = _GIT_RE.split(req)[0].strip()
-    req_name = re.split("[=<>]", req)[0].strip()
+    # Split on the first version operator. "!" and "~" are in the class so
+    # that "!=" and "~=" requirements yield the bare package name instead of a
+    # name with the operator's leading character stuck to it.
+    req_name = re.split("[=<>!~]", req)[0].strip()
     req_spec = req.removeprefix(req_name).strip().replace(" ", "")
     if "[" in req_name:
         warnings.warn(f"Cannot check optional dependencies for {req_name}")
@@ -266,7 +305,7 @@ def _check_single(
     if actual_is_git:
         # Spec has no git URL but installed dep does; name match is sufficient
         actual = _GIT_RE.split(actual)[0].strip()
-    actual_parts = re.split("[=<>]+", actual, maxsplit=1)
+    actual_parts = re.split("[=<>!~]+", actual, maxsplit=1)
     actual_name = actual_parts[0]
     actual_vers = actual_parts[1] if len(actual_parts) > 1 else ""
     if actual_name.strip().lower() != req_name.lower():
@@ -279,11 +318,33 @@ def _check_single(
     try:
         version = Version(actual_vers)
     except InvalidVersion:
-        warnings.warn(
-            f"Cannot properly check {actual_name} version {actual_vers}"
-        )
-        # TODO: Check exact version only
-        return True
+        # An unparseable actual version (e.g. conda's "9e") can't go through
+        # SpecifierSet, which needs a parsed version to order by. Equality
+        # comparisons don't need ordering, so decide those from the version
+        # strings directly.
+        exact = _unparseable_version_satisfies(req_spec, actual_vers)
+        if exact is None:
+            # Ordering constraints and wildcards are genuinely undecidable
+            # here. A bare package name accepts any version; a pinned
+            # constraint we can't confirm counts as not satisfied rather than
+            # silently passing.
+            if not req_spec:
+                warnings.warn(
+                    f"Cannot properly check {actual_name} version "
+                    f"{actual_vers}"
+                )
+                return True
+            warnings.warn(
+                f"Cannot properly check {actual_name} version {actual_vers} "
+                f"against constraint '{req_spec}'"
+            )
+            return False
+        if not exact:
+            warnings.warn(
+                f"Installed {actual_name} version {actual_vers} does not "
+                f"satisfy '{req_spec}'"
+            )
+        return exact
     spec = SpecifierSet(req_spec)
     return spec.contains(version, prereleases=editable)
 

calkit/tests/cli/main/test_core.py

@@ -2784,3 +2784,43 @@ def test_push_reports_what_was_pushed(monkeypatch, tmp_dir):
     assert sent[-1]["targets"] == ["dvc"]
     cli_core._tell_hub_we_pushed(["dvc", "docker", "git"], [])
     assert sent[-1]["targets"] == ["dvc", "docker", "git"]
+
+
+def test_push_carries_annotated_tags(tmp_dir):
+    """Annotated tags should reach the remote along with their commits.
+
+    A plain ``git push`` leaves tags behind, so a project that tags its
+    results ends up with labels that exist only on the machine that made
+    them.
+    """
+    remote = os.path.join(tmp_dir, "remote.git")
+    subprocess.check_call(["git", "init", "--bare", "-q", remote])
+    work = os.path.join(tmp_dir, "work")
+    os.makedirs(work)
+    os.chdir(work)
+    subprocess.check_call(["git", "init", "-q"])
+    subprocess.check_call(["git", "remote", "add", "origin", remote])
+    # ``calkit init`` commits what it creates, so there is a commit to tag
+    subprocess.check_call(["calkit", "init"])
+    subprocess.check_call(["git", "tag", "-a", "v0.1.0", "-m", "First"])
+    # An unannotated tag must stay local: --follow-tags is deliberately the
+    # conservative form, so scratch tags do not get published by accident
+    subprocess.check_call(["git", "tag", "scratch"])
+    subprocess.check_call(
+        [
+            "calkit",
+            "push",
+            "git",
+            "--git-arg",
+            "-u",
+            "--git-arg",
+            "origin",
+            "--git-arg",
+            "HEAD",
+        ]
+    )
+    tags = subprocess.check_output(
+        ["git", "ls-remote", "--tags", remote], text=True
+    )
+    assert "v0.1.0" in tags
+    assert "scratch" not in tags

calkit/tests/cli/test_latex.py

@@ -358,6 +358,7 @@ def test_marked_up_digest_ignores_the_header():
     assert _marked_up_digest(changed) != _marked_up_digest(first)
 
 
+@skipif_windows_docker
 def test_latex_diff_of_one_revision_against_itself(tmp_dir):
     # Two revisions that resolve to the same commit is what a pull request
     # diff looks like from the default branch. The pipeline resolves both
@@ -387,3 +388,17 @@ def test_latex_diff_of_one_revision_against_itself(tmp_dir):
         text=True,
     )
     assert "Nothing to compare" not in result.stderr
+    # A verbatim input that's a macro parameter used to make latexdiff try
+    # to open, e.g., '#1.wcsum' and fail
+    with open("paper/main.tex", "w") as f:
+        f.write("\\documentclass{article}\n\\usepackage{verbatim}\n")
+        f.write("\\newcommand{\\wc}[1]{\\verbatiminput{#1.wcsum}}\n")
+        f.write("\\begin{document}\nHi\n\\end{document}\n")
+    _commit("macro")
+    result = subprocess.run(
+        ["calkit", "latex", "diff", "paper/main.tex", "--from", sha],
+        capture_output=True,
+        text=True,
+    )
+    assert "Couldn't open" not in result.stderr
+    assert result.returncode == 0, result.stderr

calkit/tests/test_conda.py

@@ -14,6 +14,7 @@ from calkit.conda import (
     _enrich_pip_deps_from_freeze,
     _get_pip_dependency_list,
     _split_env_dependencies,
+    _unparseable_version_satisfies,
     check_env,
     find_conda_exe,
 )
@@ -77,6 +78,64 @@ def test_check_single():
         env_spec_dir=".",
         conda=False,
     )
+    # Unparseable actual version (e.g. conda's "9e"): equality and inequality
+    # are still decidable by comparing version strings, a bare name accepts any
+    # version, and an ordering constraint can't be confirmed so it counts as
+    # unsatisfied.
+    assert _check_single("jpeg", "jpeg=9e", env_spec_dir=".", conda=True)
+    assert _check_single("jpeg=9e", "jpeg=9e", env_spec_dir=".", conda=True)
+    assert _check_single("jpeg!=1", "jpeg=9e", env_spec_dir=".", conda=True)
+    assert not _check_single(
+        "jpeg!=9e", "jpeg=9e", env_spec_dir=".", conda=True
+    )
+    assert not _check_single("jpeg=1", "jpeg=9e", env_spec_dir=".", conda=True)
+    # conda's "=1.2" expands to "==1.2.*", and a wildcard needs a parsed
+    # version, so it stays unverifiable.
+    assert not _check_single(
+        "jpeg=1.2", "jpeg=9e", env_spec_dir=".", conda=True
+    )
+    assert not _check_single(
+        "jpeg>=1", "jpeg=9e", env_spec_dir=".", conda=True
+    )
+    # Pip-style specifiers behave the same way
+    assert _check_single("jpeg==9e", "jpeg==9e", env_spec_dir=".", conda=False)
+    # "!=" and "~=" must parse the package name correctly, which they didn't
+    # when the name was split on "=<>" alone
+    assert _check_single(
+        "jpeg!=1.0", "jpeg==9.0", env_spec_dir=".", conda=False
+    )
+    assert not _check_single(
+        "jpeg!=9.0", "jpeg==9.0", env_spec_dir=".", conda=False
+    )
+    assert _check_single(
+        "jpeg~=1.0", "jpeg==1.9", env_spec_dir=".", conda=False
+    )
+    assert not _check_single(
+        "jpeg~=1.0", "jpeg==2.0", env_spec_dir=".", conda=False
+    )
+
+
+def test_unparseable_version_satisfies():
+    check = _unparseable_version_satisfies
+    # No constraint accepts anything
+    assert check("", "9e") is True
+    # Plain equality and inequality compare as strings
+    assert check("==9e", "9e") is True
+    assert check("==9e", "9f") is False
+    assert check("!=9e", "9e") is False
+    assert check("!=9f", "9e") is True
+    # PEP 440 arbitrary equality is also a string comparison
+    assert check("===9e", "9e") is True
+    # Conjunctions hold only if every clause holds
+    assert check("==9e,!=9f", "9e") is True
+    assert check("==9e,==9f", "9e") is False
+    # Wildcards and ordering operators need a parsed version
+    assert check("==1.*", "9e") is None
+    assert check("!=1.*", "9e") is None
+    assert check(">=1", "9e") is None
+    assert check("~=1.2", "9e") is None
+    # Matching is exact, with no zero-padding
+    assert check("==1.0", "1.0.0") is False
 
 
 def test_enrich_pip_deps_from_freeze():

{calkit_python-0.47.2.dist-info → calkit_python-0.47.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: calkit-python
-Version: 0.47.2
+Version: 0.47.3
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://calkit.org
 Project-URL: Issues, https://github.com/calkit/calkit/issues

{calkit_python-0.47.2.dist-info → calkit_python-0.47.3.dist-info}/RECORD

@@ -1,7 +1,7 @@
 calkit/__init__.py,sha256=wZKQLIAhgCoR4vP8tWa2yFOPU9bUqE0qXWkOyFPyx1s,2920
 calkit/__main__.py,sha256=whqS7I7q_c9004emvKptZ9B9OVn-jgr5kaLaCFKmwa0,112
 calkit/calc.py,sha256=5RQVwH3goakmeDwHtmslcAZJXEZihIBuLNw_lF6QCcc,7924
-calkit/conda.py,sha256=Jb1Fz3jwkk4SZ0NgoWXd4lf50gEC8d8U87ElrYjdiwk,30752
+calkit/conda.py,sha256=ddsHScMlPkpPU-d5vi-X--ANFvO2fi0fRFUFd_Ux51Y,33399
 calkit/config.py,sha256=RS-i2Qi4OczpjzkreNfLBX8ltZqSFSKIO9aiohvqXoA,20304
 calkit/core.py,sha256=z-2lQ61bOF90FUQvDFyi8cmZfMJ03gVLiQ8z16Ert5g,52259
 calkit/datasets.py,sha256=3YtDmvBCzyX5AC-7Mb7ylnxM1mFLyTLj5CH7QqblDwA,2212
@@ -46,7 +46,7 @@ calkit/cli/describe.py,sha256=LMODpla_g7hyTI7Oi7V5dAb9WSp5nZ_4-XhSYmZP1eo,3608
 calkit/cli/dev.py,sha256=cu4QsfDiA_KurGx4WJcgA2qgfghMoZutE8kl4IZbUcM,1070
 calkit/cli/hub.py,sha256=ZBOlL7-mV57q_ynr4hPuhV7NlkKEkINSRksXD-jjiOg,2972
 calkit/cli/import_.py,sha256=QOZEfKUmqMntle47PRZhN8cs7gfWCBte_smPZqksl54,25563
-calkit/cli/latex.py,sha256=AfhEgRKVBnWFkMl-6rhEvy814biFAkHehfjdrVh6qoY,36596
+calkit/cli/latex.py,sha256=dp-bjrKvkzkKx0-k-AKqCL9HyH0a3iP0t4RoaRJUZpA,38190
 calkit/cli/list.py,sha256=CU5JCPYs7iNdzdaQoVzJcJj3cfZ_jfSdv6D048zP1Oo,18982
 calkit/cli/new.py,sha256=uoONf8jrrCx7R1tmRdInKjJGp_xeo9nTs9AzEixCe_M,158163
 calkit/cli/notebooks.py,sha256=aR4I0qatOtkrAxEG5PVLej20SBLKo8qr-lxDSzgljUQ,38836
@@ -56,7 +56,7 @@ calkit/cli/scheduler.py,sha256=s4q9wLcvTCmxuLmAoz7ptJZiNXPWCamn-NU1S5l28go,52719
 calkit/cli/sync.py,sha256=WlY5XwoS_KGJ2s7hZhsowcg73Y0L3YDKzYzbZp8obUw,12485
 calkit/cli/update.py,sha256=A1QWp1G69rMJkW058NbW29OXPZYEcKvuVW9WvBOqMso,53738
 calkit/cli/main/__init__.py,sha256=qu1POZPyqs33ZKfasOxv_Wc-EzVcEgK3Dt_vwFL8Bi8,65
-calkit/cli/main/core.py,sha256=8o1WzYjjadq6jUsRkKSUf_98pkW-qx-131xwUXvM7-Y,170778
+calkit/cli/main/core.py,sha256=01dw513Qd3aJGCpQ_zu2QqMoQrNpF1lKz9HfWw-xFpg,171107
 calkit/cli/main/xr.py,sha256=cYQBNVlRTzp6ba3EwEwZylOxVpk9ThWhy6IAD7_ahWw,37594
 calkit/dvc/__init__.py,sha256=-B6tilCb_jw7QFmJ2srILez24wDhNKUzIBhZUMt01dE,381
 calkit/dvc/core.py,sha256=R6Fm65ZwG_yq0PNN3kfiMaQV_fba0B7MEkWHOhY8xhk,39505
@@ -97,7 +97,7 @@ calkit/templates/latex/jfm/upmath.sty,sha256=9nzNixqQd18zVrv0vLBjGjfnc8L19tP_m0b
 calkit/templates/latex/report/paper.tex,sha256=Sc_ZrBKg6DK_xjjUKkiHTjYXl0HoxSrJkwYgtcDJakA,1037
 calkit/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 calkit/tests/test_calc.py,sha256=h-wOUIRqfyi06LTzhY_rS-a1xChZTkmwdEfBybMUM7E,2033
-calkit/tests/test_conda.py,sha256=me6nteGTmI6rN9xqHwn44OqkERCRUqLx57NnHeOpd8M,14433
+calkit/tests/test_conda.py,sha256=-TMM_IKptQgmD8VZmS_6X67Ig9A2qMcSSCRKoHBtYbQ,16995
 calkit/tests/test_config.py,sha256=m08u_2IG4c391Vn_MYdJ4QS1w4PBHctUQa4IG7EsH6k,13656
 calkit/tests/test_core.py,sha256=FpQWshX_0XxCqDB9-HEqtnktZ_yvfz7MIyhywAzEqzI,14697
 calkit/tests/test_dependencies.py,sha256=Stb_pQr8HTrkUSTjZFAJ2aFOXAzlFNXtEjf2Uh0PF2E,12672
@@ -139,7 +139,7 @@ calkit/tests/cli/test_delete.py,sha256=qIbgwKc8nBjmkynzyVuVAjrQB96XSmGRet_jfxs19
 calkit/tests/cli/test_describe.py,sha256=uJ6r11Wkh1oVkPB-U9Kt5ktCSDFLTSL0OCIHy43sWIU,2657
 calkit/tests/cli/test_hub.py,sha256=z3ne8Bnjv-V85OEh15FbAV4STrFwZKMgl_DgWwQ2wzY,7385
 calkit/tests/cli/test_import.py,sha256=snQgCw6SM9V3g5NS8oBK-2B3bYFVyJcuXtJuFtDtfA8,13441
-calkit/tests/cli/test_latex.py,sha256=z6Y7OQp7n_FBMnTdQJD-qT5q268zBK7Up5eEcpS65oo,12566
+calkit/tests/cli/test_latex.py,sha256=gzFaAf-u68fm-e5DORUd_d-mKOaINfa_BObbtQp7_4Y,13219
 calkit/tests/cli/test_list.py,sha256=5jc_OYI_rXNVv2UQc6IS8ItjQbBwEI5IDw5xKU_Uk98,9165
 calkit/tests/cli/test_new.py,sha256=Hpo7cHPyxWRVQF1JVkznO3YPhw9YxI92f017xLeHZLc,75600
 calkit/tests/cli/test_notebooks.py,sha256=2t1KiGhEz9H9LcIdWy4jGM05REUxJpWiIg6fSpX12ME,10678
@@ -148,7 +148,7 @@ calkit/tests/cli/test_scheduler.py,sha256=YfJi_fcRlQt1bdFyo3b8BFelA1PcH-wn5lAVXi
 calkit/tests/cli/test_sync.py,sha256=jmhfgoMIjdihIuu9UVyHSizBDTF0hlBt2VWqEdVkAKk,4375
 calkit/tests/cli/test_update.py,sha256=S2pBvJg8GCGVxie_eG9e176-opO43lKtHTvLK0x63ck,17783
 calkit/tests/cli/main/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-calkit/tests/cli/main/test_core.py,sha256=Vy75WNMW5_N-BfoBAfrTG_P3NM5I5OOugn3Ronx7Tyk,103717
+calkit/tests/cli/main/test_core.py,sha256=4Z294o-9IkljrKgZid8THkhifIZBeHTBCgVcgC77n-0,105126
 calkit/tests/cli/main/test_lock.py,sha256=1iX8iSbGtr4O9OkaAi4d3gP3_QzNl6Rr6HLtbEpS6iU,9847
 calkit/tests/cli/main/test_subprojects.py,sha256=Qs5NvwhQEFlZUvAtOyCWN243PONz8N79np5HwlgUl7E,18709
 calkit/tests/cli/main/test_xr.py,sha256=iauAWKXdzaaRFu5W91l4ZdH_ZU3h2NAn3v5p-EhAbco,28798
@@ -168,22 +168,22 @@ calkit/agent_skills/check-questions/SKILL.md,sha256=WlQWWuS-TgsoDU504WdLR6UW3Grc
 calkit/agent_skills/check-reproducibility/SKILL.md,sha256=5SGmtnbq8bSJW0Zwav_aVzfuhilHwBkkdxGuZvPHxGU,4699
 calkit/agent_skills/conventions/SKILL.md,sha256=kK0Sa54uIORAslE3U53sXJUG-TMdM-Ie72hCMIzzbxQ,8909
 calkit/agent_skills/create-pipeline/SKILL.md,sha256=2FGw1iDQVRk5FUq79GP3lPdgvgof2Wi1O9O-abGGtgs,5422
-calkit_python-0.47.2.data/data/etc/jupyter/jupyter_server_config.d/calkit.json,sha256=CWrZP--JDGz8fsvbAlKr_duTL1vDriGT48SL1YCtkY0,81
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