From 1e4cf5f1ae820d441e09d851faf301cb705c213a Mon Sep 17 00:00:00 2001
From: joshkamm <joshkamm@umich.edu>
Date: Wed, 30 Oct 2024 03:51:43 -0400
Subject: [PATCH 01/10] add pytest environment to pixi.toml

add python file to start playing with pytest
---
 examples/geom_1/test_output.py |   2 +
 pixi.lock                      | 488 +++++++++++++++++++++++++++++++++
 pixi.toml                      |  12 +
 3 files changed, 502 insertions(+)
 create mode 100644 examples/geom_1/test_output.py

diff --git a/examples/geom_1/test_output.py b/examples/geom_1/test_output.py
new file mode 100644
index 0000000..ae2a896
--- /dev/null
+++ b/examples/geom_1/test_output.py
@@ -0,0 +1,2 @@
+def test_output():
+    assert True
\ No newline at end of file
diff --git a/pixi.lock b/pixi.lock
index 25ad1aa..b68a2d7 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -209,6 +209,55 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2024b-hc8b5060_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda
+  pytest:
+    channels:
+    - url: https://conda.anaconda.org/nvidia/
+    - url: https://conda.anaconda.org/conda-forge/
+    packages:
+      linux-64:
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.8.30-hbcca054_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/cmake-3.30.5-hf9cb763_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.2-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.0.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.10.1-hbbe4b11_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.3-h5888daf_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h77fa898_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-h4bc722e_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.64.0-h161d5f1_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.47.0-hadc24fc_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.2.0-hc0a3c3a_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.2.0-h4852527_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libuv-1.49.2-hb9d3cd8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-he02047a_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.2-hb9d3cd8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-24.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/pluggy-1.5.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/pytest-8.3.3-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.13.0-h9ebbce0_100_cp313.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.13-5_cp313.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/rhash-1.4.5-hb9d3cd8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.2-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2024b-hc8b5060_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda
 packages:
 - kind: conda
   name: _libgcc_mutex
@@ -418,6 +467,46 @@ packages:
   license_family: BSD
   size: 19707706
   timestamp: 1727459501915
+- kind: conda
+  name: cmake
+  version: 3.30.5
+  build: hf9cb763_0
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/cmake-3.30.5-hf9cb763_0.conda
+  sha256: 9b775bbdee337d67b180b6fbc6c93fa1ba73a18b167c242d792dee2797245148
+  md5: b3b88a7ec6372b6f2c0ddb31ee009ebd
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - bzip2 >=1.0.8,<2.0a0
+  - libcurl >=8.10.1,<9.0a0
+  - libexpat >=2.6.3,<3.0a0
+  - libgcc >=13
+  - libstdcxx >=13
+  - libuv >=1.49.0,<2.0a0
+  - libzlib >=1.3.1,<2.0a0
+  - ncurses >=6.5,<7.0a0
+  - rhash >=1.4.4,<2.0a0
+  - xz >=5.2.6,<6.0a0
+  - zstd >=1.5.6,<1.6.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 19606674
+  timestamp: 1728416480376
+- kind: conda
+  name: colorama
+  version: 0.4.6
+  build: pyhd8ed1ab_0
+  subdir: noarch
+  noarch: python
+  url: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2
+  sha256: 2c1b2e9755ce3102bca8d69e8f26e4f087ece73f50418186aee7c74bef8e1698
+  md5: 3faab06a954c2a04039983f2c4a50d99
+  depends:
+  - python >=3.7
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 25170
+  timestamp: 1666700778190
 - kind: conda
   name: cuda
   version: 12.6.2
@@ -1205,6 +1294,20 @@ packages:
   license: LicenseRef-NVIDIA-End-User-License-Agreement
   size: 16965
   timestamp: 1726770278034
+- kind: conda
+  name: exceptiongroup
+  version: 1.2.2
+  build: pyhd8ed1ab_0
+  subdir: noarch
+  noarch: python
+  url: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.2-pyhd8ed1ab_0.conda
+  sha256: e0edd30c4b7144406bb4da975e6bb97d6bc9c0e999aa4efe66ae108cada5d5b5
+  md5: d02ae936e42063ca46af6cdad2dbd1e0
+  depends:
+  - python >=3.7
+  license: MIT and PSF-2.0
+  size: 20418
+  timestamp: 1720869435725
 - kind: conda
   name: gcc_impl_linux-64
   version: 12.4.0
@@ -1311,6 +1414,21 @@ packages:
   license_family: BSD
   size: 30317
   timestamp: 1727281506580
+- kind: conda
+  name: iniconfig
+  version: 2.0.0
+  build: pyhd8ed1ab_0
+  subdir: noarch
+  noarch: python
+  url: https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.0.0-pyhd8ed1ab_0.conda
+  sha256: 38740c939b668b36a50ef455b077e8015b8c9cf89860d421b3fff86048f49666
+  md5: f800d2da156d08e289b14e87e43c1ae5
+  depends:
+  - python >=3.7
+  license: MIT
+  license_family: MIT
+  size: 11101
+  timestamp: 1673103208955
 - kind: conda
   name: kernel-headers_linux-64
   version: 3.10.0
@@ -1408,6 +1526,23 @@ packages:
   license_family: GPL
   size: 669616
   timestamp: 1727304687962
+- kind: conda
+  name: ld_impl_linux-64
+  version: '2.43'
+  build: h712a8e2_2
+  build_number: 2
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_2.conda
+  sha256: 7c91cea91b13f4314d125d1bedb9d03a29ebbd5080ccdea70260363424646dbe
+  md5: 048b02e3962f066da18efe3a21b77672
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  constrains:
+  - binutils_impl_linux-64 2.43
+  license: GPL-3.0-only
+  license_family: GPL
+  size: 669211
+  timestamp: 1729655358674
 - kind: conda
   name: libcublas
   version: 12.6.3.3
@@ -1760,6 +1895,21 @@ packages:
   license_family: MIT
   size: 72342
   timestamp: 1725568840022
+- kind: conda
+  name: libffi
+  version: 3.4.2
+  build: h7f98852_5
+  build_number: 5
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2
+  sha256: ab6e9856c21709b7b517e940ae7028ae0737546122f83c2aa5d692860c3b149e
+  md5: d645c6d2ac96843a2bfaccd2d62b3ac3
+  depends:
+  - libgcc-ng >=9.4.0
+  license: MIT
+  license_family: MIT
+  size: 58292
+  timestamp: 1636488182923
 - kind: conda
   name: libgcc
   version: 14.1.0
@@ -1797,6 +1947,25 @@ packages:
   license_family: GPL
   size: 533503
   timestamp: 1724802540921
+- kind: conda
+  name: libgcc
+  version: 14.2.0
+  build: h77fa898_1
+  build_number: 1
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda
+  sha256: 53eb8a79365e58849e7b1a068d31f4f9e718dc938d6f2c03e960345739a03569
+  md5: 3cb76c3f10d3bc7f1105b2fc9db984df
+  depends:
+  - _libgcc_mutex 0.1 conda_forge
+  - _openmp_mutex >=4.5
+  constrains:
+  - libgomp 14.2.0 h77fa898_1
+  - libgcc-ng ==14.2.0=*_1
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 848745
+  timestamp: 1729027721139
 - kind: conda
   name: libgcc-devel_linux-64
   version: 12.4.0
@@ -1843,6 +2012,21 @@ packages:
   license_family: GPL
   size: 52203
   timestamp: 1724802545317
+- kind: conda
+  name: libgcc-ng
+  version: 14.2.0
+  build: h69a702a_1
+  build_number: 1
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_1.conda
+  sha256: 3a76969c80e9af8b6e7a55090088bc41da4cffcde9e2c71b17f44d37b7cb87f7
+  md5: e39480b9ca41323497b05492a63bc35b
+  depends:
+  - libgcc 14.2.0 h77fa898_1
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 54142
+  timestamp: 1729027726517
 - kind: conda
   name: libgfortran-ng
   version: 7.5.0
@@ -1901,6 +2085,36 @@ packages:
   license_family: GPL
   size: 461429
   timestamp: 1724802428910
+- kind: conda
+  name: libgomp
+  version: 14.2.0
+  build: h77fa898_1
+  build_number: 1
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h77fa898_1.conda
+  sha256: 1911c29975ec99b6b906904040c855772ccb265a1c79d5d75c8ceec4ed89cd63
+  md5: cc3573974587f12dda90d96e3e55a702
+  depends:
+  - _libgcc_mutex 0.1 conda_forge
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 460992
+  timestamp: 1729027639220
+- kind: conda
+  name: libmpdec
+  version: 4.0.0
+  build: h4bc722e_0
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-h4bc722e_0.conda
+  sha256: d02d1d3304ecaf5c728e515eb7416517a0b118200cd5eacbe829c432d1664070
+  md5: aeb98fdeb2e8f25d43ef71fbacbeec80
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc-ng >=12
+  license: BSD-2-Clause
+  license_family: BSD
+  size: 89991
+  timestamp: 1723817448345
 - kind: conda
   name: libnghttp2
   version: 1.58.0
@@ -1943,6 +2157,27 @@ packages:
   license_family: MIT
   size: 677508
   timestamp: 1702130071743
+- kind: conda
+  name: libnghttp2
+  version: 1.64.0
+  build: h161d5f1_0
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.64.0-h161d5f1_0.conda
+  sha256: b0f2b3695b13a989f75d8fd7f4778e1c7aabe3b36db83f0fe80b2cd812c0e975
+  md5: 19e57602824042dfd0446292ef90488b
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - c-ares >=1.32.3,<2.0a0
+  - libev >=4.33,<4.34.0a0
+  - libev >=4.33,<5.0a0
+  - libgcc >=13
+  - libstdcxx >=13
+  - libzlib >=1.3.1,<2.0a0
+  - openssl >=3.3.2,<4.0a0
+  license: MIT
+  license_family: MIT
+  size: 647599
+  timestamp: 1729571887612
 - kind: conda
   name: libnpp
   version: 12.3.1.54
@@ -2097,6 +2332,22 @@ packages:
   license_family: GPL
   size: 3947704
   timestamp: 1724801833649
+- kind: conda
+  name: libsqlite
+  version: 3.47.0
+  build: hadc24fc_1
+  build_number: 1
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.47.0-hadc24fc_1.conda
+  sha256: 8a9aadf996a2399f65b679c6e7f29139d5059f699c63e6d7b50e20db10c00508
+  md5: b6f02b52a174e612e89548f4663ce56a
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  - libzlib >=1.3.1,<2.0a0
+  license: Unlicense
+  size: 875349
+  timestamp: 1730208050020
 - kind: conda
   name: libssh2
   version: 1.11.0
@@ -2159,6 +2410,21 @@ packages:
   license_family: GPL
   size: 3892781
   timestamp: 1724801863728
+- kind: conda
+  name: libstdcxx
+  version: 14.2.0
+  build: hc0a3c3a_1
+  build_number: 1
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.2.0-hc0a3c3a_1.conda
+  sha256: 4661af0eb9bdcbb5fb33e5d0023b001ad4be828fccdcc56500059d56f9869462
+  md5: 234a5554c53625688d51062645337328
+  depends:
+  - libgcc 14.2.0 h77fa898_1
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 3893695
+  timestamp: 1729027746910
 - kind: conda
   name: libstdcxx-devel_linux-64
   version: 12.4.0
@@ -2205,6 +2471,35 @@ packages:
   license_family: GPL
   size: 52240
   timestamp: 1724802596264
+- kind: conda
+  name: libstdcxx-ng
+  version: 14.2.0
+  build: h4852527_1
+  build_number: 1
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.2.0-h4852527_1.conda
+  sha256: 25bb30b827d4f6d6f0522cc0579e431695503822f144043b93c50237017fffd8
+  md5: 8371ac6457591af2cf6159439c1fd051
+  depends:
+  - libstdcxx 14.2.0 hc0a3c3a_1
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 54105
+  timestamp: 1729027780628
+- kind: conda
+  name: libuuid
+  version: 2.38.1
+  build: h0b41bf4_0
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda
+  sha256: 787eb542f055a2b3de553614b25f09eefb0a0931b0c87dbcce6efdfd92f04f18
+  md5: 40b61aab5c7ba9ff276c41cfffe6b80b
+  depends:
+  - libgcc-ng >=12
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 33601
+  timestamp: 1680112270483
 - kind: conda
   name: libuv
   version: 1.49.0
@@ -2234,6 +2529,21 @@ packages:
   license_family: MIT
   size: 878395
   timestamp: 1727283212868
+- kind: conda
+  name: libuv
+  version: 1.49.2
+  build: hb9d3cd8_0
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libuv-1.49.2-hb9d3cd8_0.conda
+  sha256: a35cd81cd1a9add11024097da83cc06b0aae83186fe4124b77710876f37d8f31
+  md5: 070e3c9ddab77e38799d5c30b109c633
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  license: MIT
+  license_family: MIT
+  size: 884647
+  timestamp: 1729322566955
 - kind: conda
   name: libzlib
   version: 1.3.1
@@ -2268,6 +2578,24 @@ packages:
   license_family: Other
   size: 67199
   timestamp: 1716874136348
+- kind: conda
+  name: libzlib
+  version: 1.3.1
+  build: hb9d3cd8_2
+  build_number: 2
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda
+  sha256: d4bfe88d7cb447768e31650f06257995601f89076080e76df55e3112d4e47dc4
+  md5: edb0dca6bc32e4f4789199455a1dbeb8
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  constrains:
+  - zlib 1.3.1 *_2
+  license: Zlib
+  license_family: Other
+  size: 60963
+  timestamp: 1727963148474
 - kind: conda
   name: mpi
   version: '1.0'
@@ -2367,6 +2695,120 @@ packages:
   license_family: Apache
   size: 2891789
   timestamp: 1725410790053
+- kind: conda
+  name: packaging
+  version: '24.1'
+  build: pyhd8ed1ab_0
+  subdir: noarch
+  noarch: python
+  url: https://conda.anaconda.org/conda-forge/noarch/packaging-24.1-pyhd8ed1ab_0.conda
+  sha256: 36aca948219e2c9fdd6d80728bcc657519e02f06c2703d8db3446aec67f51d81
+  md5: cbe1bb1f21567018ce595d9c2be0f0db
+  depends:
+  - python >=3.8
+  license: Apache-2.0
+  license_family: APACHE
+  size: 50290
+  timestamp: 1718189540074
+- kind: conda
+  name: pluggy
+  version: 1.5.0
+  build: pyhd8ed1ab_0
+  subdir: noarch
+  noarch: python
+  url: https://conda.anaconda.org/conda-forge/noarch/pluggy-1.5.0-pyhd8ed1ab_0.conda
+  sha256: 33eaa3359948a260ebccf9cdc2fd862cea5a6029783289e13602d8e634cd9a26
+  md5: d3483c8fc2dc2cc3f5cf43e26d60cabf
+  depends:
+  - python >=3.8
+  license: MIT
+  license_family: MIT
+  size: 23815
+  timestamp: 1713667175451
+- kind: conda
+  name: pytest
+  version: 8.3.3
+  build: pyhd8ed1ab_0
+  subdir: noarch
+  noarch: python
+  url: https://conda.anaconda.org/conda-forge/noarch/pytest-8.3.3-pyhd8ed1ab_0.conda
+  sha256: e99376d0068455712109d233f5790458ff861aeceb458bfda74e353338e4d815
+  md5: c03d61f31f38fdb9facf70c29958bf7a
+  depends:
+  - colorama
+  - exceptiongroup >=1.0.0rc8
+  - iniconfig
+  - packaging
+  - pluggy <2,>=1.5
+  - python >=3.8
+  - tomli >=1
+  constrains:
+  - pytest-faulthandler >=2
+  license: MIT
+  license_family: MIT
+  size: 258293
+  timestamp: 1725977334143
+- kind: conda
+  name: python
+  version: 3.13.0
+  build: h9ebbce0_100_cp313
+  build_number: 100
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/python-3.13.0-h9ebbce0_100_cp313.conda
+  sha256: 6ab5179679f0909db828d8316f3b8b379014a82404807310fe7df5a6cf303646
+  md5: 08e9aef080f33daeb192b2ddc7e4721f
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - bzip2 >=1.0.8,<2.0a0
+  - ld_impl_linux-64 >=2.36.1
+  - libexpat >=2.6.3,<3.0a0
+  - libffi >=3.4,<4.0a0
+  - libgcc >=13
+  - libmpdec >=4.0.0,<5.0a0
+  - libsqlite >=3.46.1,<4.0a0
+  - libuuid >=2.38.1,<3.0a0
+  - libzlib >=1.3.1,<2.0a0
+  - ncurses >=6.5,<7.0a0
+  - openssl >=3.3.2,<4.0a0
+  - python_abi 3.13.* *_cp313
+  - readline >=8.2,<9.0a0
+  - tk >=8.6.13,<8.7.0a0
+  - tzdata
+  - xz >=5.2.6,<6.0a0
+  license: Python-2.0
+  size: 33112481
+  timestamp: 1728419573472
+- kind: conda
+  name: python_abi
+  version: '3.13'
+  build: 5_cp313
+  build_number: 5
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.13-5_cp313.conda
+  sha256: 438225b241c5f9bddae6f0178a97f5870a89ecf927dfca54753e689907331442
+  md5: 381bbd2a92c863f640a55b6ff3c35161
+  constrains:
+  - python 3.13.* *_cp313
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 6217
+  timestamp: 1723823393322
+- kind: conda
+  name: readline
+  version: '8.2'
+  build: h8228510_1
+  build_number: 1
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda
+  sha256: 5435cf39d039387fbdc977b0a762357ea909a7694d9528ab40f005e9208744d7
+  md5: 47d31b792659ce70f470b5c82fdfb7a4
+  depends:
+  - libgcc-ng >=12
+  - ncurses >=6.3,<7.0a0
+  license: GPL-3.0-only
+  license_family: GPL
+  size: 281456
+  timestamp: 1679532220005
 - kind: conda
   name: rhash
   version: 1.4.4
@@ -2395,6 +2837,21 @@ packages:
   license_family: MIT
   size: 185144
   timestamp: 1693455923632
+- kind: conda
+  name: rhash
+  version: 1.4.5
+  build: hb9d3cd8_0
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/rhash-1.4.5-hb9d3cd8_0.conda
+  sha256: 04677caac29ec64a5d41d0cca8dbec5f60fa166d5458ff5a4393e4dc08a4799e
+  md5: 9af0e7981755f09c81421946c4bcea04
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  license: MIT
+  license_family: MIT
+  size: 186921
+  timestamp: 1728886721623
 - kind: conda
   name: sysroot_linux-64
   version: '2.17'
@@ -2412,6 +2869,37 @@ packages:
   license_family: GPL
   size: 15141219
   timestamp: 1727437660028
+- kind: conda
+  name: tk
+  version: 8.6.13
+  build: noxft_h4845f30_101
+  build_number: 101
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda
+  sha256: e0569c9caa68bf476bead1bed3d79650bb080b532c64a4af7d8ca286c08dea4e
+  md5: d453b98d9c83e71da0741bb0ff4d76bc
+  depends:
+  - libgcc-ng >=12
+  - libzlib >=1.2.13,<2.0.0a0
+  license: TCL
+  license_family: BSD
+  size: 3318875
+  timestamp: 1699202167581
+- kind: conda
+  name: tomli
+  version: 2.0.2
+  build: pyhd8ed1ab_0
+  subdir: noarch
+  noarch: python
+  url: https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.2-pyhd8ed1ab_0.conda
+  sha256: 5e742ba856168b606ac3c814d247657b1c33b8042371f1a08000bdc5075bc0cc
+  md5: e977934e00b355ff55ed154904044727
+  depends:
+  - python >=3.7
+  license: MIT
+  license_family: MIT
+  size: 18203
+  timestamp: 1727974767524
 - kind: conda
   name: tzdata
   version: 2024b
diff --git a/pixi.toml b/pixi.toml
index 6221132..82e82f6 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -19,10 +19,18 @@ description = "Test SlaterGPU executable on a small molecular system"
 cwd = "build/examples/geom_1"
 cmd = "/export/SLURM/default/bin/srun -p zimA10 -N1 -n1 -c2 --gpus=1 ../sgpu.exe"
 
+[feature.pytest.tasks.pytest]
+description = "Invoke pytest to sanity check output from test task"
+depends-on = ["test"]
+cwd = "build/examples/geom_1"
+cmd = "pytest"
+
 [feature.athena]
 platforms = ["linux-64"]
 [feature.linux-64]
 platforms = ["linux-64"]
+[feature.pytest]
+platforms = ["linux-64"]
 
 [feature.athena.tasks]
 slurm-job = "/export/SLURM/default/bin/srun -p zimA10 -N1 -n16 --gpus=1 --pty /bin/bash"
@@ -158,6 +166,10 @@ openmpi = "=3.1"
 # openmpi-mpicc = "=3.1"
 # openmpi-mpicxx = "=3.1"
 
+[feature.pytest.dependencies]
+pytest = ">=8.3.3,<9"
+
 [environments]
 athena = {features = ["athena"]}
 linux-64 = {features = ["linux-64"]}
+pytest = {features = ["pytest"]}

From cf0f67cc15df190c0253490be401eb5a77cc2a2a Mon Sep 17 00:00:00 2001
From: joshkamm <joshkamm@umich.edu>
Date: Wed, 6 Nov 2024 02:32:01 -0500
Subject: [PATCH 02/10] #11 adding pytest to pixi start command

---
 pixi.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pixi.toml b/pixi.toml
index 82e82f6..1a97aad 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -6,13 +6,13 @@ platforms = ["linux-64", "linux-aarch64"]
 
 [tasks]
 clean = {cmd = "rm -rf build", description = "Delete build directory"}
-build = {cmd = "cmake --build build -j 16", description = "Invoke cmake to compile and link the executable"}
+build = {cmd = "cmake --build build -j 32", description = "Invoke cmake to compile and link the executable"}
 start-linux-64 = {depends-on = ["configure-linux-64", "build", "test"]}
 
 [tasks.start-athena]
 description = "Configure, build, and test on the Zimmerman group cluster"
 cmd = "echo 'Finished pixi start-athena!'"
-depends-on = ["configure-athena", "build", "test"]
+depends-on = ["configure-athena", "build", "pytest"]
 
 [tasks.test]
 description = "Test SlaterGPU executable on a small molecular system"

From c2cf043b73a73f7401607d5699d1172191d92c9a Mon Sep 17 00:00:00 2001
From: joshkamm <joshkamm@umich.edu>
Date: Thu, 7 Nov 2024 03:27:20 -0500
Subject: [PATCH 03/10] #11 flesh out pytest for geom_1 example

add numpy to pixi pytest environment
---
 examples/geom_1/test_output.py |  18 ++-
 pixi.lock                      | 222 ++++++++++++++++++++++++++++-----
 pixi.toml                      |   5 +-
 3 files changed, 210 insertions(+), 35 deletions(-)

diff --git a/examples/geom_1/test_output.py b/examples/geom_1/test_output.py
index ae2a896..81643da 100644
--- a/examples/geom_1/test_output.py
+++ b/examples/geom_1/test_output.py
@@ -1,2 +1,18 @@
+import os
+from pathlib import Path
+import numpy as np
+import pytest
+
+
 def test_output():
-    assert True
\ No newline at end of file
+    # convert from script location to corresponding location in build directory
+    script_dir = Path(os.path.abspath(__file__)).parent
+    script_dir_parts = list(script_dir.parts)
+    script_dir_parts.insert(-2, "build")
+    script_build_dir = Path(*script_dir_parts)
+
+    assert script_build_dir.exists()
+    A = np.loadtxt(script_build_dir / "A", skiprows=1)
+    A_ref = np.loadtxt(script_build_dir / "A_ref", skiprows=1)
+    assert A.shape == A_ref.shape
+    assert A == pytest.approx(A_ref)
diff --git a/pixi.lock b/pixi.lock
index b68a2d7..faf0748 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -227,6 +227,8 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-25_linux64_openblas.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-25_linux64_openblas.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.10.1-hbbe4b11_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda
@@ -234,23 +236,29 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-14.2.0-h69a702a_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.2.0-hd5240d6_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h77fa898_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-h4bc722e_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-25_linux64_openblas.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.64.0-h161d5f1_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.28-pthreads_h94d23a6_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.47.0-hadc24fc_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.2.0-hc0a3c3a_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.2.0-h4852527_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libuv-1.49.2-hb9d3cd8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-he02047a_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.1.3-py312h58c1407_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.2-hb9d3cd8_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-24.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pluggy-1.5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pytest-8.3.3-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.13.0-h9ebbce0_100_cp313.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.13-5_cp313.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.7-hc5c86c4_0_cpython.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/rhash-1.4.5-hb9d3cd8_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda
@@ -1543,6 +1551,46 @@ packages:
   license_family: GPL
   size: 669211
   timestamp: 1729655358674
+- kind: conda
+  name: libblas
+  version: 3.9.0
+  build: 25_linux64_openblas
+  build_number: 25
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-25_linux64_openblas.conda
+  sha256: d6d12dc437d060f838820e9e61bf73baab651f91935ac594cf10beb9ef1b4450
+  md5: 8ea26d42ca88ec5258802715fe1ee10b
+  depends:
+  - libopenblas >=0.3.28,<0.3.29.0a0
+  - libopenblas >=0.3.28,<1.0a0
+  constrains:
+  - liblapack 3.9.0 25_linux64_openblas
+  - libcblas 3.9.0 25_linux64_openblas
+  - blas * openblas
+  - liblapacke 3.9.0 25_linux64_openblas
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 15677
+  timestamp: 1729642900350
+- kind: conda
+  name: libcblas
+  version: 3.9.0
+  build: 25_linux64_openblas
+  build_number: 25
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-25_linux64_openblas.conda
+  sha256: ab87b0477078837c91d9cda62a9faca18fba7c57cc77aa779ae24b3ac783b5dd
+  md5: 5dbd1b0fc0d01ec5e0e1fbe667281a11
+  depends:
+  - libblas 3.9.0 25_linux64_openblas
+  constrains:
+  - liblapack 3.9.0 25_linux64_openblas
+  - blas * openblas
+  - liblapacke 3.9.0 25_linux64_openblas
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 15613
+  timestamp: 1729642905619
 - kind: conda
   name: libcublas
   version: 12.6.3.3
@@ -2027,6 +2075,23 @@ packages:
   license_family: GPL
   size: 54142
   timestamp: 1729027726517
+- kind: conda
+  name: libgfortran
+  version: 14.2.0
+  build: h69a702a_1
+  build_number: 1
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-14.2.0-h69a702a_1.conda
+  sha256: fc9e7f22a17faf74da904ebfc4d88699013d2992e55505e4aa0eb01770290977
+  md5: f1fd30127802683586f768875127a987
+  depends:
+  - libgfortran5 14.2.0 hd5240d6_1
+  constrains:
+  - libgfortran-ng ==14.2.0=*_1
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 53997
+  timestamp: 1729027752995
 - kind: conda
   name: libgfortran-ng
   version: 7.5.0
@@ -2057,6 +2122,23 @@ packages:
   license_family: GPL
   size: 1309697
   timestamp: 1644093800802
+- kind: conda
+  name: libgfortran5
+  version: 14.2.0
+  build: hd5240d6_1
+  build_number: 1
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.2.0-hd5240d6_1.conda
+  sha256: d149a37ca73611e425041f33b9d8dbed6e52ec506fe8cc1fc0ee054bddeb6d5d
+  md5: 9822b874ea29af082e5d36098d25427d
+  depends:
+  - libgcc >=14.2.0
+  constrains:
+  - libgfortran 14.2.0
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 1462645
+  timestamp: 1729027735353
 - kind: conda
   name: libgomp
   version: 14.1.0
@@ -2101,20 +2183,24 @@ packages:
   size: 460992
   timestamp: 1729027639220
 - kind: conda
-  name: libmpdec
-  version: 4.0.0
-  build: h4bc722e_0
+  name: liblapack
+  version: 3.9.0
+  build: 25_linux64_openblas
+  build_number: 25
   subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-h4bc722e_0.conda
-  sha256: d02d1d3304ecaf5c728e515eb7416517a0b118200cd5eacbe829c432d1664070
-  md5: aeb98fdeb2e8f25d43ef71fbacbeec80
+  url: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-25_linux64_openblas.conda
+  sha256: 9d1ff017714edb2d84868f0f931a4a0e7c289a971062b2ac66cfc8145df7e20e
+  md5: 4dc03a53fc69371a6158d0ed37214cd3
   depends:
-  - __glibc >=2.17,<3.0.a0
-  - libgcc-ng >=12
-  license: BSD-2-Clause
+  - libblas 3.9.0 25_linux64_openblas
+  constrains:
+  - liblapacke 3.9.0 25_linux64_openblas
+  - libcblas 3.9.0 25_linux64_openblas
+  - blas * openblas
+  license: BSD-3-Clause
   license_family: BSD
-  size: 89991
-  timestamp: 1723817448345
+  size: 15608
+  timestamp: 1729642910812
 - kind: conda
   name: libnghttp2
   version: 1.58.0
@@ -2213,6 +2299,20 @@ packages:
   license: LicenseRef-NVIDIA-End-User-License-Agreement
   size: 450976
   timestamp: 1723660954045
+- kind: conda
+  name: libnsl
+  version: 2.0.1
+  build: hd590300_0
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda
+  sha256: 26d77a3bb4dceeedc2a41bd688564fe71bf2d149fdcf117049970bc02ff1add6
+  md5: 30fd6e37fe21f86f4bd26d6ee73eeec7
+  depends:
+  - libgcc-ng >=12
+  license: LGPL-2.1-only
+  license_family: GPL
+  size: 33408
+  timestamp: 1697359010159
 - kind: conda
   name: libnvfatbin
   version: 12.6.77
@@ -2316,6 +2416,26 @@ packages:
   license: LicenseRef-NVIDIA-End-User-License-Agreement
   size: 27438
   timestamp: 1723657907832
+- kind: conda
+  name: libopenblas
+  version: 0.3.28
+  build: pthreads_h94d23a6_1
+  build_number: 1
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.28-pthreads_h94d23a6_1.conda
+  sha256: 99ba271d8a80a1af2723f2e124ffd91d850074c0389c067e6d96d72a2dbfeabe
+  md5: 62857b389e42b36b686331bec0922050
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - libgfortran
+  - libgfortran5 >=14.2.0
+  constrains:
+  - openblas >=0.3.28,<0.3.29.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 5578513
+  timestamp: 1730772671118
 - kind: conda
   name: libsanitizer
   version: 12.4.0
@@ -2544,6 +2664,20 @@ packages:
   license_family: MIT
   size: 884647
   timestamp: 1729322566955
+- kind: conda
+  name: libxcrypt
+  version: 4.4.36
+  build: hd590300_1
+  build_number: 1
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda
+  sha256: 6ae68e0b86423ef188196fff6207ed0c8195dd84273cb5623b85aa08033a410c
+  md5: 5aa797f8787fe7a17d1b0821485b5adc
+  depends:
+  - libgcc-ng >=12
+  license: LGPL-2.1-or-later
+  size: 100393
+  timestamp: 1702724383534
 - kind: conda
   name: libzlib
   version: 1.3.1
@@ -2647,6 +2781,29 @@ packages:
   md5: 217ed2ff255f52cbef787aba3f9b9637
   size: 699526661
   timestamp: 1709778043113
+- kind: conda
+  name: numpy
+  version: 2.1.3
+  build: py312h58c1407_0
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.1.3-py312h58c1407_0.conda
+  sha256: e4c14f71588a5627a6935d3e7d9ca78a8387229ec8ebc91616b0988ce57ba0dc
+  md5: dfdbc12e6d81889ba4c494a23f23eba8
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libblas >=3.9.0,<4.0a0
+  - libcblas >=3.9.0,<4.0a0
+  - libgcc >=13
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx >=13
+  - python >=3.12,<3.13.0a0
+  - python_abi 3.12.* *_cp312
+  constrains:
+  - numpy-base <0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 8388631
+  timestamp: 1730588649810
 - kind: conda
   name: openmpi
   version: 3.1.4
@@ -2750,13 +2907,12 @@ packages:
   timestamp: 1725977334143
 - kind: conda
   name: python
-  version: 3.13.0
-  build: h9ebbce0_100_cp313
-  build_number: 100
+  version: 3.12.7
+  build: hc5c86c4_0_cpython
   subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/python-3.13.0-h9ebbce0_100_cp313.conda
-  sha256: 6ab5179679f0909db828d8316f3b8b379014a82404807310fe7df5a6cf303646
-  md5: 08e9aef080f33daeb192b2ddc7e4721f
+  url: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.7-hc5c86c4_0_cpython.conda
+  sha256: 674be31ff152d9f0e0fe16959a45e3803a730fc4f54d87df6a9ac4e6a698c41d
+  md5: 0515111a9cdf69f83278f7c197db9807
   depends:
   - __glibc >=2.17,<3.0.a0
   - bzip2 >=1.0.8,<2.0a0
@@ -2764,35 +2920,37 @@ packages:
   - libexpat >=2.6.3,<3.0a0
   - libffi >=3.4,<4.0a0
   - libgcc >=13
-  - libmpdec >=4.0.0,<5.0a0
+  - libnsl >=2.0.1,<2.1.0a0
   - libsqlite >=3.46.1,<4.0a0
   - libuuid >=2.38.1,<3.0a0
+  - libxcrypt >=4.4.36
   - libzlib >=1.3.1,<2.0a0
   - ncurses >=6.5,<7.0a0
   - openssl >=3.3.2,<4.0a0
-  - python_abi 3.13.* *_cp313
   - readline >=8.2,<9.0a0
   - tk >=8.6.13,<8.7.0a0
   - tzdata
   - xz >=5.2.6,<6.0a0
+  constrains:
+  - python_abi 3.12.* *_cp312
   license: Python-2.0
-  size: 33112481
-  timestamp: 1728419573472
+  size: 31574780
+  timestamp: 1728059777603
 - kind: conda
   name: python_abi
-  version: '3.13'
-  build: 5_cp313
+  version: '3.12'
+  build: 5_cp312
   build_number: 5
   subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.13-5_cp313.conda
-  sha256: 438225b241c5f9bddae6f0178a97f5870a89ecf927dfca54753e689907331442
-  md5: 381bbd2a92c863f640a55b6ff3c35161
+  url: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda
+  sha256: d10e93d759931ffb6372b45d65ff34d95c6000c61a07e298d162a3bc2accebb0
+  md5: 0424ae29b104430108f5218a66db7260
   constrains:
-  - python 3.13.* *_cp313
+  - python 3.12.* *_cpython
   license: BSD-3-Clause
   license_family: BSD
-  size: 6217
-  timestamp: 1723823393322
+  size: 6238
+  timestamp: 1723823388266
 - kind: conda
   name: readline
   version: '8.2'
diff --git a/pixi.toml b/pixi.toml
index 1a97aad..030db39 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -17,12 +17,12 @@ depends-on = ["configure-athena", "build", "pytest"]
 [tasks.test]
 description = "Test SlaterGPU executable on a small molecular system"
 cwd = "build/examples/geom_1"
-cmd = "/export/SLURM/default/bin/srun -p zimA10 -N1 -n1 -c2 --gpus=1 ../sgpu.exe"
+cmd = "/export/SLURM/default/bin/srun -p zim2080 -N1 -n1 -c2 --gpus=1 ../sgpu.exe"
 
 [feature.pytest.tasks.pytest]
 description = "Invoke pytest to sanity check output from test task"
 depends-on = ["test"]
-cwd = "build/examples/geom_1"
+cwd = "examples/geom_1"
 cmd = "pytest"
 
 [feature.athena]
@@ -168,6 +168,7 @@ openmpi = "=3.1"
 
 [feature.pytest.dependencies]
 pytest = ">=8.3.3,<9"
+numpy = ">=2.1.3,<3"
 
 [environments]
 athena = {features = ["athena"]}

From ac429783d29d6ed697befe164f29fc3df0107eb5 Mon Sep 17 00:00:00 2001
From: joshkamm <joshkamm@umich.edu>
Date: Fri, 8 Nov 2024 02:57:25 -0500
Subject: [PATCH 04/10] #11 set relative and absolute tolerances when comparing
 output

---
 examples/geom_1/test_output.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/geom_1/test_output.py b/examples/geom_1/test_output.py
index 81643da..0a748fc 100644
--- a/examples/geom_1/test_output.py
+++ b/examples/geom_1/test_output.py
@@ -15,4 +15,4 @@ def test_output():
     A = np.loadtxt(script_build_dir / "A", skiprows=1)
     A_ref = np.loadtxt(script_build_dir / "A_ref", skiprows=1)
     assert A.shape == A_ref.shape
-    assert A == pytest.approx(A_ref)
+    assert A == pytest.approx(A_ref, rel=1e-3, abs=1e-6)

From e59e15ceb93ca3f3e28a414c63621096bee6dd7a Mon Sep 17 00:00:00 2001
From: joshkamm <joshkamm@umich.edu>
Date: Fri, 8 Nov 2024 18:23:34 -0500
Subject: [PATCH 05/10] #11 update relative tolerance based on conversation
 with Paul

---
 examples/geom_1/test_output.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/geom_1/test_output.py b/examples/geom_1/test_output.py
index 0a748fc..3da3ccb 100644
--- a/examples/geom_1/test_output.py
+++ b/examples/geom_1/test_output.py
@@ -15,4 +15,4 @@ def test_output():
     A = np.loadtxt(script_build_dir / "A", skiprows=1)
     A_ref = np.loadtxt(script_build_dir / "A_ref", skiprows=1)
     assert A.shape == A_ref.shape
-    assert A == pytest.approx(A_ref, rel=1e-3, abs=1e-6)
+    assert A == pytest.approx(A_ref, rel=1e-6, abs=1e-6)

From 339c8c62be78a32e08002a7662e5354319831ac9 Mon Sep 17 00:00:00 2001
From: joshkamm <joshkamm@umich.edu>
Date: Fri, 15 Nov 2024 02:22:51 -0500
Subject: [PATCH 06/10] #11 move file with pytests

---
 examples/{geom_1 => }/test_output.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename examples/{geom_1 => }/test_output.py (100%)

diff --git a/examples/geom_1/test_output.py b/examples/test_output.py
similarity index 100%
rename from examples/geom_1/test_output.py
rename to examples/test_output.py

From 389fe020504c52dc468895f3dbf546f93df3adfa Mon Sep 17 00:00:00 2001
From: joshkamm <joshkamm@umich.edu>
Date: Fri, 15 Nov 2024 03:09:36 -0500
Subject: [PATCH 07/10] #11 parametrize pytest to check multiple integral files

move location of pytest file from specific example to examples folder
add pycache to gitignore
---
 .gitignore              |  1 +
 examples/test_output.py | 20 +++++++++-----------
 pixi.toml               |  2 +-
 3 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/.gitignore b/.gitignore
index 33b0354..1ea1673 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,7 @@ compile_commands.json
 CTestTestfile.cmake
 _deps
 build*
+/examples/__pycache__
 # pixi environments
 .pixi
 *.egg-info
diff --git a/examples/test_output.py b/examples/test_output.py
index 3da3ccb..4cca058 100644
--- a/examples/test_output.py
+++ b/examples/test_output.py
@@ -3,16 +3,14 @@
 import numpy as np
 import pytest
 
-
-def test_output():
-    # convert from script location to corresponding location in build directory
+@pytest.mark.parametrize("filename", ["A", "Ciap", "pVp"])
+def test_output(filename):
+    # convert from script location to where the output files should be located
     script_dir = Path(os.path.abspath(__file__)).parent
-    script_dir_parts = list(script_dir.parts)
-    script_dir_parts.insert(-2, "build")
-    script_build_dir = Path(*script_dir_parts)
+    example_output_dir = script_dir.parent / "build" / "examples" / "geom_1"
 
-    assert script_build_dir.exists()
-    A = np.loadtxt(script_build_dir / "A", skiprows=1)
-    A_ref = np.loadtxt(script_build_dir / "A_ref", skiprows=1)
-    assert A.shape == A_ref.shape
-    assert A == pytest.approx(A_ref, rel=1e-6, abs=1e-6)
+    assert example_output_dir.exists()
+    output = np.loadtxt(example_output_dir / filename, skiprows=1)
+    reference_output = np.loadtxt(example_output_dir / f"{filename}_ref", skiprows=1)
+    assert output.shape == reference_output.shape
+    assert output == pytest.approx(reference_output, rel=1e-6, abs=1e-6)
diff --git a/pixi.toml b/pixi.toml
index 030db39..b12de8e 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -22,7 +22,7 @@ cmd = "/export/SLURM/default/bin/srun -p zim2080 -N1 -n1 -c2 --gpus=1 ../sgpu.ex
 [feature.pytest.tasks.pytest]
 description = "Invoke pytest to sanity check output from test task"
 depends-on = ["test"]
-cwd = "examples/geom_1"
+cwd = "examples"
 cmd = "pytest"
 
 [feature.athena]

From 472d48f646558441a6c9819b66f4d3bdadb69736 Mon Sep 17 00:00:00 2001
From: joshkamm <joshkamm@umich.edu>
Date: Sat, 16 Nov 2024 20:27:07 -0500
Subject: [PATCH 08/10] #11 wip allowing for comparing multiple matrices as in
 SENT

---
 examples/test_output.py | 22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/examples/test_output.py b/examples/test_output.py
index 4cca058..703d510 100644
--- a/examples/test_output.py
+++ b/examples/test_output.py
@@ -10,7 +10,21 @@ def test_output(filename):
     example_output_dir = script_dir.parent / "build" / "examples" / "geom_1"
 
     assert example_output_dir.exists()
-    output = np.loadtxt(example_output_dir / filename, skiprows=1)
-    reference_output = np.loadtxt(example_output_dir / f"{filename}_ref", skiprows=1)
-    assert output.shape == reference_output.shape
-    assert output == pytest.approx(reference_output, rel=1e-6, abs=1e-6)
+
+    with open(example_output_dir / filename) as output, open(
+        example_output_dir / f"{filename}_ref"
+    ) as reference_output:
+        output = list(output)
+        for i, line in enumerate(reference_output):
+            if line.endswith(":"):
+                continue
+            assert np.fromstring(output[i], sep=" ") == pytest.approx(
+                np.fromstring(line, sep=" "), rel=1e-6, abs=1e-6
+            )
+        # matrix_boundaries = [line for line in file if line.endswith(':')] + [-1]
+    # for idx in range(len(matrix_boundaries)-1):
+
+    # output = np.loadtxt(example_output_dir / filename, skiprows=matrix_boundaries[idx])
+    # reference_output = np.loadtxt(example_output_dir / f"{filename}_ref", skiprows=matrix_boundaries[idx]+1, max_rows=matrix_boundaries[idx+1]-matrix_boundaries[idx])
+    # assert output.shape == reference_output.shape
+    # assert output == pytest.approx(reference_output, rel=1e-6, abs=1e-6)

From 4bfea6dad162d1739026a349d79d03a1d22d9a99 Mon Sep 17 00:00:00 2001
From: joshkamm <joshkamm@umich.edu>
Date: Tue, 19 Nov 2024 02:40:11 -0500
Subject: [PATCH 09/10] #11 wip reading multiple matrices from same file

---
 examples/test_output.py | 51 ++++++++++++++++++++++++++---------------
 pixi.toml               |  2 +-
 2 files changed, 34 insertions(+), 19 deletions(-)

diff --git a/examples/test_output.py b/examples/test_output.py
index 703d510..a8326b1 100644
--- a/examples/test_output.py
+++ b/examples/test_output.py
@@ -1,3 +1,4 @@
+from itertools import pairwise
 import os
 from pathlib import Path
 import numpy as np
@@ -5,26 +6,40 @@
 
 @pytest.mark.parametrize("filename", ["A", "Ciap", "pVp"])
 def test_output(filename):
-    # convert from script location to where the output files should be located
+    # Convert from the script location to where the output files should be located.
     script_dir = Path(os.path.abspath(__file__)).parent
     example_output_dir = script_dir.parent / "build" / "examples" / "geom_1"
 
     assert example_output_dir.exists()
 
-    with open(example_output_dir / filename) as output, open(
-        example_output_dir / f"{filename}_ref"
-    ) as reference_output:
-        output = list(output)
-        for i, line in enumerate(reference_output):
-            if line.endswith(":"):
-                continue
-            assert np.fromstring(output[i], sep=" ") == pytest.approx(
-                np.fromstring(line, sep=" "), rel=1e-6, abs=1e-6
-            )
-        # matrix_boundaries = [line for line in file if line.endswith(':')] + [-1]
-    # for idx in range(len(matrix_boundaries)-1):
-
-    # output = np.loadtxt(example_output_dir / filename, skiprows=matrix_boundaries[idx])
-    # reference_output = np.loadtxt(example_output_dir / f"{filename}_ref", skiprows=matrix_boundaries[idx]+1, max_rows=matrix_boundaries[idx+1]-matrix_boundaries[idx])
-    # assert output.shape == reference_output.shape
-    # assert output == pytest.approx(reference_output, rel=1e-6, abs=1e-6)
+    with open(example_output_dir / f"{filename}_ref") as reference_output:
+        # output = list(output)
+        # for i, line in enumerate(reference_output):
+        # if line.endswith(":"):
+        #     continue
+        # assert np.fromstring(output[i], sep=" ") == pytest.approx(
+        #     np.fromstring(line, sep=" "), rel=1e-6, abs=1e-6
+        # )
+        matrix_boundaries = [
+            line_num
+            for line_num, line in enumerate(reference_output)
+            # Get header lines for matrices and blank last line.
+            if line.strip().endswith(":")
+        ] + [len(reference_output)]  # JOSH - RESUME HERE
+    print(f"{matrix_boundaries = }")
+    for header_row, end_row in pairwise(matrix_boundaries):
+        start_row = header_row + 1
+        num_rows = end_row - start_row
+        output = np.loadtxt(
+            example_output_dir / filename,
+            skiprows=start_row,
+            max_rows=num_rows,
+        )
+        reference_output = np.loadtxt(
+            example_output_dir / f"{filename}_ref",
+            skiprows=start_row,
+            max_rows=num_rows,
+        )
+        assert output.shape == reference_output.shape
+        assert output + 1 == pytest.approx(reference_output, rel=1e-6, abs=1e-6)
+    assert False
diff --git a/pixi.toml b/pixi.toml
index b12de8e..ccb72e9 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -173,4 +173,4 @@ numpy = ">=2.1.3,<3"
 [environments]
 athena = {features = ["athena"]}
 linux-64 = {features = ["linux-64"]}
-pytest = {features = ["pytest"]}
+pytest = {features = ["pytest", "athena"]}

From 6dc5a88072ffa661b24af0ceb329b3850ce9511a Mon Sep 17 00:00:00 2001
From: joshkamm <joshkamm@umich.edu>
Date: Wed, 20 Nov 2024 04:09:01 -0500
Subject: [PATCH 10/10] #11 comparing multiple matrices in same file

---
 examples/test_output.py | 36 ++++++++++++++----------------------
 1 file changed, 14 insertions(+), 22 deletions(-)

diff --git a/examples/test_output.py b/examples/test_output.py
index a8326b1..3908ac7 100644
--- a/examples/test_output.py
+++ b/examples/test_output.py
@@ -4,42 +4,34 @@
 import numpy as np
 import pytest
 
-@pytest.mark.parametrize("filename", ["A", "Ciap", "pVp"])
+@pytest.mark.parametrize("filename", ["A", "Ciap", "pVp", "SENT"])
 def test_output(filename):
     # Convert from the script location to where the output files should be located.
     script_dir = Path(os.path.abspath(__file__)).parent
     example_output_dir = script_dir.parent / "build" / "examples" / "geom_1"
 
-    assert example_output_dir.exists()
-
     with open(example_output_dir / f"{filename}_ref") as reference_output:
-        # output = list(output)
-        # for i, line in enumerate(reference_output):
-        # if line.endswith(":"):
-        #     continue
-        # assert np.fromstring(output[i], sep=" ") == pytest.approx(
-        #     np.fromstring(line, sep=" "), rel=1e-6, abs=1e-6
-        # )
-        matrix_boundaries = [
-            line_num
-            for line_num, line in enumerate(reference_output)
-            # Get header lines for matrices and blank last line.
-            if line.strip().endswith(":")
-        ] + [len(reference_output)]  # JOSH - RESUME HERE
-    print(f"{matrix_boundaries = }")
+        reference_output_lines = reference_output.readlines()
+
+    matrix_boundaries = [
+        line_num
+        for line_num, line in enumerate(reference_output_lines)
+        # Get header lines for matrices and blank last line.
+        if line.strip().endswith(":")
+    ] + [len(reference_output_lines)]
+
+    # Loop over each matrix in the file and compare to the reference.
     for header_row, end_row in pairwise(matrix_boundaries):
         start_row = header_row + 1
         num_rows = end_row - start_row
-        output = np.loadtxt(
+        matrix = np.loadtxt(
             example_output_dir / filename,
             skiprows=start_row,
             max_rows=num_rows,
         )
-        reference_output = np.loadtxt(
+        reference_matrix = np.loadtxt(
             example_output_dir / f"{filename}_ref",
             skiprows=start_row,
             max_rows=num_rows,
         )
-        assert output.shape == reference_output.shape
-        assert output + 1 == pytest.approx(reference_output, rel=1e-6, abs=1e-6)
-    assert False
+        assert matrix == pytest.approx(reference_matrix, rel=1e-6, abs=1e-6)