Updates to support numpy 1.24 and newer

[codecov[bot]]

Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (ace29a8) 94.93% compared to head (db8c649) 94.95%. Report is 3 commits behind head on master.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #280 +/- ## ========================================== + Coverage 94.93% 94.95% +0.02% ========================================== Files 374 375 +1 Lines 23883 24020 +137 ========================================== + Hits 22673 22809 +136 - Misses 1210 1211 +1 ``` | [Flag](https://app.codecov.io/gh/uw-ipd/tmol/pull/280/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | Coverage Δ | | |---|---|---| | [_shrug_Testing_CPU](https://app.codecov.io/gh/uw-ipd/tmol/pull/280/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | `90.17% <86.30%> (+0.14%)` | :arrow_up: | | [_shrug_Testing_CPU_debug_w_o_jit](https://app.codecov.io/gh/uw-ipd/tmol/pull/280/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | `91.96% <86.30%> (?)` | | | [_shrug_Testing_CPU_w_o_jit](https://app.codecov.io/gh/uw-ipd/tmol/pull/280/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | `?` | | | [_shrug_Testing_CUDA](https://app.codecov.io/gh/uw-ipd/tmol/pull/280/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | `92.41% <98.21%> (+0.03%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files](https://app.codecov.io/gh/uw-ipd/tmol/pull/280?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | Coverage Δ | | |---|---|---| | [tmol/io/details/build\_missing\_leaf\_atoms.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/280?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9pby9kZXRhaWxzL2J1aWxkX21pc3NpbmdfbGVhZl9hdG9tcy5weQ==) | `99.30% <100.00%> (ø)` | | | [tmol/io/details/select\_from\_canonical.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/280?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9pby9kZXRhaWxzL3NlbGVjdF9mcm9tX2Nhbm9uaWNhbC5weQ==) | `99.24% <100.00%> (+<0.01%)` | :arrow_up: | | [tmol/io/write\_pose\_stack\_pdb.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/280?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9pby93cml0ZV9wb3NlX3N0YWNrX3BkYi5weQ==) | `86.86% <100.00%> (ø)` | | | [tmol/pose/compiled/apsp\_ops.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/280?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9wb3NlL2NvbXBpbGVkL2Fwc3Bfb3BzLnB5) | `100.00% <100.00%> (ø)` | | | [tmol/pose/pose\_stack\_builder.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/280?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9wb3NlL3Bvc2Vfc3RhY2tfYnVpbGRlci5weQ==) | `97.61% <100.00%> (ø)` | | | [tmol/score/modules/dunbrack.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/280?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9zY29yZS9tb2R1bGVzL2R1bmJyYWNrLnB5) | `99.19% <100.00%> (ø)` | | | [tmol/tests/data/\_\_init\_\_.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/280?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC90ZXN0cy9kYXRhL19faW5pdF9fLnB5) | `89.53% <100.00%> (ø)` | | | [.../tests/io/details/test\_build\_missing\_leaf\_atoms.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/280?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC90ZXN0cy9pby9kZXRhaWxzL3Rlc3RfYnVpbGRfbWlzc2luZ19sZWFmX2F0b21zLnB5) | `100.00% <100.00%> (ø)` | | | [...mol/tests/io/details/test\_select\_from\_canonical.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/280?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC90ZXN0cy9pby9kZXRhaWxzL3Rlc3Rfc2VsZWN0X2Zyb21fY2Fub25pY2FsLnB5) | `98.10% <100.00%> (+0.02%)` | :arrow_up: | | [tmol/tests/io/test\_pose\_stack\_construction.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/280?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC90ZXN0cy9pby90ZXN0X3Bvc2Vfc3RhY2tfY29uc3RydWN0aW9uLnB5) | `100.00% <100.00%> (ø)` | | | ... and [8 more](https://app.codecov.io/gh/uw-ipd/tmol/pull/280?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/uw-ipd/tmol/pull/280/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd)

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