安装问题

[hyShen-hzau]

您好，我游览了您发表在iMate上的文章，并且非常感兴趣想要学习jcvi。但是在安装的途中重复出现这样的错误，希望能得到您的帮助。
(base) [newshy@zhaolabserver jcvi]$ conda activate jcvi
(jcvi) [newshy@zhaolabserver jcvi]$ pip install jcvi
Collecting jcvi
Using cached jcvi-1.5.4.tar.gz (785 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... error
error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [137 lines of output]
/tmp/pip-build-env-b0q4sasw/overlay/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: project.license as a TOML table is deprecated
!!

          ********************************************************************************
          Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

          By 2026-Feb-18, you need to update your project and remove deprecated calls
          or your builds will no longer be supported.

          See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
          ********************************************************************************

  !!
    corresp(dist, value, root_dir)
  running build_ext
  Compiling src/jcvi/assembly/chic.pyx because it changed.
  [1/1] Cythonizing src/jcvi/assembly/chic.pyx
  building 'jcvi.assembly.chic' extension
  creating build/temp.linux-x86_64-cpython-312/src/jcvi/assembly
  gcc -pthread -B /data_SSD/home/newshy/miniconda3/envs/jcvi/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /data_SSD/home/newshy/miniconda3/envs/jcvi/include -fPIC -O2 -isystem /data_SSD/home/newshy/miniconda3/envs/jcvi/include -fPIC -I/tmp/pip-build-env-b0q4sasw/overlay/lib/python3.12/site-packages/numpy/_core/include -I/data_SSD/home/newshy/miniconda3/envs/jcvi/include/python3.12 -c src/jcvi/assembly/chic.c -o build/temp.linux-x86_64-cpython-312/src/jcvi/assembly/chic.o -O3
  In file included from /tmp/pip-build-env-b0q4sasw/overlay/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1913:0,
                   from /tmp/pip-build-env-b0q4sasw/overlay/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-b0q4sasw/overlay/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h:5,
                   from src/jcvi/assembly/chic.c:1140:
  /tmp/pip-build-env-b0q4sasw/overlay/lib/python3.12/site-packages/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it with " \
    ^
  src/jcvi/assembly/chic.c: In function ‘__pyx_pw_4jcvi_8assembly_4chic_1score_evaluate_M’:
  src/jcvi/assembly/chic.c:6086:7: error: ‘for’ loop initial declarations are only allowed in C99 mode
         for (Py_ssize_t i = __pyx_nargs; i < 1; i++) {
         ^
  src/jcvi/assembly/chic.c:6086:7: note: use option -std=c99 or -std=gnu99 to compile your code
  src/jcvi/assembly/chic.c:6134:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c:6158:19: error: redefinition of ‘__pyx_temp’
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6134:19: note: previous definition of ‘__pyx_temp’ was here
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6158:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c:6163:19: error: redefinition of ‘__pyx_temp’
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6158:19: note: previous definition of ‘__pyx_temp’ was here
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6163:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c: In function ‘__pyx_pw_4jcvi_8assembly_4chic_3score_evaluate_P’:
  src/jcvi/assembly/chic.c:6645:7: error: ‘for’ loop initial declarations are only allowed in C99 mode
         for (Py_ssize_t i = __pyx_nargs; i < 1; i++) {
         ^
  src/jcvi/assembly/chic.c:6693:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c:6717:19: error: redefinition of ‘__pyx_temp’
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6693:19: note: previous definition of ‘__pyx_temp’ was here
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6717:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c:6722:19: error: redefinition of ‘__pyx_temp’
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6717:19: note: previous definition of ‘__pyx_temp’ was here
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6722:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c: In function ‘__pyx_pw_4jcvi_8assembly_4chic_5score_evaluate_Q’:
  src/jcvi/assembly/chic.c:7228:7: error: ‘for’ loop initial declarations are only allowed in C99 mode
         for (Py_ssize_t i = __pyx_nargs; i < 1; i++) {
         ^
  src/jcvi/assembly/chic.c:7276:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c:7300:19: error: redefinition of ‘__pyx_temp’
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:7276:19: note: previous definition of ‘__pyx_temp’ was here
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:7300:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c:7305:19: error: redefinition of ‘__pyx_temp’
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:7300:19: note: previous definition of ‘__pyx_temp’ was here
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:7305:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c: In function ‘__Pyx_ParseKeywordsTuple’:
  src/jcvi/assembly/chic.c:10029:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
       for (Py_ssize_t pos = 0; pos < num_kwargs; pos++) {
       ^
  In file included from src/jcvi/assembly/chic.c:12731:0:
  /data_SSD/home/newshy/miniconda3/envs/jcvi/include/python3.12/internal/pycore_frame.h: In function ‘_PyFrame_Initialize’:
  /data_SSD/home/newshy/miniconda3/envs/jcvi/include/python3.12/internal/pycore_frame.h:132:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
       for (int i = null_locals_from; i < code->co_nlocalsplus; i++) {
       ^
  src/jcvi/assembly/chic.c: In function ‘__Pyx_PyCode_New’:
  src/jcvi/assembly/chic.c:14283:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
       for (Py_ssize_t i=0; i < var_count; i++) {
       ^
  error: command '/usr/bin/gcc' failed with exit code 1
  Using custom wheel tag: cp312-cp312-linux_x86_64
  Traceback (most recent call last):
    File "/data_SSD/home/newshy/miniconda3/envs/jcvi/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
      main()
    File "/data_SSD/home/newshy/miniconda3/envs/jcvi/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
      json_out["return_val"] = hook(**hook_input["kwargs"])
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/data_SSD/home/newshy/miniconda3/envs/jcvi/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 178, in prepare_metadata_for_build_wheel
      whl_basename = backend.build_wheel(metadata_directory, config_settings)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-b0q4sasw/overlay/lib/python3.12/site-packages/hatchling/build.py", line 58, in build_wheel
      return os.path.basename(next(builder.build(directory=wheel_directory, versions=['standard'])))
                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-b0q4sasw/overlay/lib/python3.12/site-packages/hatchling/builders/plugin/interface.py", line 147, in build
      build_hook.initialize(version, build_data)
    File "/tmp/pip-install-64v_p0x8/jcvi_a7a4f88b500649a0925fa29f816eb924/build.py", line 13, in initialize
      subprocess.check_call(["python", "setup.py", "build_ext", "--inplace"])
    File "/data_SSD/home/newshy/miniconda3/envs/jcvi/lib/python3.12/subprocess.py", line 413, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['python', 'setup.py', 'build_ext', '--inplace']' returned non-zero exit status 1.
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

[Adamtaranto]

Tried to fix this in #760 but Hatchling is rejecting valid SPDX strings in the format that setuptools is migrating to.

See: pypa/hatch#1708

I don't think this should be happening with python 3.12.

What version of setup tools are you using?

[hyShen-hzau]

我的python版本为3.12.0
(jcvi) [newshy@zhaolabserver jcvi]$ python -V
Python 3.12.0

[hyShen-hzau]

抱歉没有回答setup tool的版本，setup tool的Version: 80.8.0
(jcvi) [newshy@zhaolabserver jcvi]$ pip show setuptools
Name: setuptools
Version: 80.8.0
Summary: Easily download, build, install, upgrade, and uninstall Python packages
Home-page:
Author:
Author-email: Python Packaging Authority distutils-sig@python.org
License-Expression: MIT
Location: /data_SSD/home/newshy/miniconda3/envs/jcvi/lib/python3.12/site-packages
Requires:
Required-by:

[Adamtaranto]

Try downgrading to setuptools<=77.0.0

[hyShen-hzau]

我将setuptools版本降级到了76.0.0，可惜还是安装报错。报错相同。

(jcvi) [newshy@zhaolabserver jcvi]$ pip show setuptools
Name: setuptools
Version: 76.0.0
Summary: Easily download, build, install, upgrade, and uninstall Python packages
Home-page:
Author:
Author-email: Python Packaging Authority distutils-sig@python.org
License:
Location: /data_SSD/home/newshy/miniconda3/envs/jcvi/lib/python3.12/site-packages
Requires:
Required-by:
(jcvi) [newshy@zhaolabserver jcvi]$ conda activate jcvi
(jcvi) [newshy@zhaolabserver jcvi]$ pip install git+git://github.com/tanghaibao/jcvi.git
Collecting git+git://github.com/tanghaibao/jcvi.git
Cloning git://github.com/tanghaibao/jcvi.git to /tmp/pip-req-build-mz7sy_bl
Running command git clone --filter=blob:none --quiet git://github.com/tanghaibao/jcvi.git /tmp/pip-req-build-mz7sy_bl
fatal: unable to connect to github.com:
github.com[0: 20.205.243.166]: errno=Connection timed out

error: subprocess-exited-with-error

× git clone --filter=blob:none --quiet git://github.com/tanghaibao/jcvi.git /tmp/pip-req-build-mz7sy_bl did not run successfully.
│ exit code: 128
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× git clone --filter=blob:none --quiet git://github.com/tanghaibao/jcvi.git /tmp/pip-req-build-mz7sy_bl did not run successfully.
│ exit code: 128
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

[Adamtaranto]

typo in the readme, fixed.

pip install git+https://github.com/tanghaibao/jcvi.git

[hyShen-hzau]

非常感谢您耐心的解答，我使用这个代码获得了相同的报错。我会继续尝试其它的安装方式。
(jcvi) [newshy@zhaolabserver jcvi]$ pip install git+https://github.com/tanghaibao/jcvi.git
Collecting git+https://github.com/tanghaibao/jcvi.git
Cloning https://github.com/tanghaibao/jcvi.git to /tmp/pip-req-build-0alh2qby
Running command git clone --filter=blob:none --quiet https://github.com/tanghaibao/jcvi.git /tmp/pip-req-build-0alh2qby
Resolved https://github.com/tanghaibao/jcvi.git to commit 6e6f5c0
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... error
error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [137 lines of output]
/tmp/pip-build-env-44kf_gjj/overlay/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: project.license as a TOML table is deprecated
!!

          ********************************************************************************
          Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

          By 2026-Feb-18, you need to update your project and remove deprecated calls
          or your builds will no longer be supported.

          See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
          ********************************************************************************

  !!
    corresp(dist, value, root_dir)
  running build_ext
  Compiling src/jcvi/assembly/chic.pyx because it changed.
  [1/1] Cythonizing src/jcvi/assembly/chic.pyx
  building 'jcvi.assembly.chic' extension
  creating build/temp.linux-x86_64-cpython-312/src/jcvi/assembly
  gcc -pthread -B /data_SSD/home/newshy/miniconda3/envs/jcvi/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /data_SSD/home/newshy/miniconda3/envs/jcvi/include -fPIC -O2 -isystem /data_SSD/home/newshy/miniconda3/envs/jcvi/include -fPIC -I/tmp/pip-build-env-44kf_gjj/overlay/lib/python3.12/site-packages/numpy/_core/include -I/data_SSD/home/newshy/miniconda3/envs/jcvi/include/python3.12 -c src/jcvi/assembly/chic.c -o build/temp.linux-x86_64-cpython-312/src/jcvi/assembly/chic.o -O3
  In file included from /tmp/pip-build-env-44kf_gjj/overlay/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1913:0,
                   from /tmp/pip-build-env-44kf_gjj/overlay/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-44kf_gjj/overlay/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h:5,
                   from src/jcvi/assembly/chic.c:1140:
  /tmp/pip-build-env-44kf_gjj/overlay/lib/python3.12/site-packages/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it with " \
    ^
  src/jcvi/assembly/chic.c: In function ‘__pyx_pw_4jcvi_8assembly_4chic_1score_evaluate_M’:
  src/jcvi/assembly/chic.c:6086:7: error: ‘for’ loop initial declarations are only allowed in C99 mode
         for (Py_ssize_t i = __pyx_nargs; i < 1; i++) {
         ^
  src/jcvi/assembly/chic.c:6086:7: note: use option -std=c99 or -std=gnu99 to compile your code
  src/jcvi/assembly/chic.c:6134:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c:6158:19: error: redefinition of ‘__pyx_temp’
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6134:19: note: previous definition of ‘__pyx_temp’ was here
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6158:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c:6163:19: error: redefinition of ‘__pyx_temp’
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6158:19: note: previous definition of ‘__pyx_temp’ was here
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6163:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c: In function ‘__pyx_pw_4jcvi_8assembly_4chic_3score_evaluate_P’:
  src/jcvi/assembly/chic.c:6645:7: error: ‘for’ loop initial declarations are only allowed in C99 mode
         for (Py_ssize_t i = __pyx_nargs; i < 1; i++) {
         ^
  src/jcvi/assembly/chic.c:6693:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c:6717:19: error: redefinition of ‘__pyx_temp’
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6693:19: note: previous definition of ‘__pyx_temp’ was here
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6717:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c:6722:19: error: redefinition of ‘__pyx_temp’
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6717:19: note: previous definition of ‘__pyx_temp’ was here
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:6722:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c: In function ‘__pyx_pw_4jcvi_8assembly_4chic_5score_evaluate_Q’:
  src/jcvi/assembly/chic.c:7228:7: error: ‘for’ loop initial declarations are only allowed in C99 mode
         for (Py_ssize_t i = __pyx_nargs; i < 1; i++) {
         ^
  src/jcvi/assembly/chic.c:7276:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c:7300:19: error: redefinition of ‘__pyx_temp’
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:7276:19: note: previous definition of ‘__pyx_temp’ was here
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:7300:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c:7305:19: error: redefinition of ‘__pyx_temp’
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:7300:19: note: previous definition of ‘__pyx_temp’ was here
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
                     ^
  src/jcvi/assembly/chic.c:7305:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (Py_ssize_t __pyx_temp=0; __pyx_temp < (Py_ssize_t)(sizeof(values)/sizeof(values[0])); ++__pyx_temp) {
     ^
  src/jcvi/assembly/chic.c: In function ‘__Pyx_ParseKeywordsTuple’:
  src/jcvi/assembly/chic.c:10029:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
       for (Py_ssize_t pos = 0; pos < num_kwargs; pos++) {
       ^
  In file included from src/jcvi/assembly/chic.c:12731:0:
  /data_SSD/home/newshy/miniconda3/envs/jcvi/include/python3.12/internal/pycore_frame.h: In function ‘_PyFrame_Initialize’:
  /data_SSD/home/newshy/miniconda3/envs/jcvi/include/python3.12/internal/pycore_frame.h:132:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
       for (int i = null_locals_from; i < code->co_nlocalsplus; i++) {
       ^
  src/jcvi/assembly/chic.c: In function ‘__Pyx_PyCode_New’:
  src/jcvi/assembly/chic.c:14283:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
       for (Py_ssize_t i=0; i < var_count; i++) {
       ^
  error: command '/usr/bin/gcc' failed with exit code 1
  Using custom wheel tag: cp312-cp312-linux_x86_64
  Traceback (most recent call last):
    File "/data_SSD/home/newshy/miniconda3/envs/jcvi/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
      main()
    File "/data_SSD/home/newshy/miniconda3/envs/jcvi/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
      json_out["return_val"] = hook(**hook_input["kwargs"])
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/data_SSD/home/newshy/miniconda3/envs/jcvi/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 178, in prepare_metadata_for_build_wheel
      whl_basename = backend.build_wheel(metadata_directory, config_settings)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-44kf_gjj/overlay/lib/python3.12/site-packages/hatchling/build.py", line 58, in build_wheel
      return os.path.basename(next(builder.build(directory=wheel_directory, versions=['standard'])))
                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-44kf_gjj/overlay/lib/python3.12/site-packages/hatchling/builders/plugin/interface.py", line 147, in build
      build_hook.initialize(version, build_data)
    File "/tmp/pip-req-build-0alh2qby/build.py", line 13, in initialize
      subprocess.check_call(["python", "setup.py", "build_ext", "--inplace"])
    File "/data_SSD/home/newshy/miniconda3/envs/jcvi/lib/python3.12/subprocess.py", line 413, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['python', 'setup.py', 'build_ext', '--inplace']' returned non-zero exit status 1.
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with

[Adamtaranto]

Looks like there is an issue with compiling Cython modules in your env.

# Delete your existing jcvi env
# and delete any existing clone of the jcvi project repo
conda env remove -n jcvi

# Create new conda env
conda create -n jcvi -c conda-forge -c bioconda python=3.12 bedtools imagemagick libmagic wand

# Activate the new env
conda activate jcvi

# Install pre-built wheels from pypi
pip install jcvi

# If that does not work try:
pip install setuptools<=77.0.0
pip install jcvi

I was not able to replicate these issues on a osx-arm64 Mac or linux. What OS are you using?