From 30f15f00a4a0086083d4dc7fcf589a3c02244399 Mon Sep 17 00:00:00 2001 From: LGTM Migrator Date: Tue, 8 Nov 2022 17:33:58 +0000 Subject: [PATCH 1/6] Add CodeQL workflow for GitHub code scanning --- .github/workflows/codeql.yml | 41 ++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 .github/workflows/codeql.yml diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml new file mode 100644 index 0000000..199bf35 --- /dev/null +++ b/.github/workflows/codeql.yml @@ -0,0 +1,41 @@ +name: "CodeQL" + +on: + push: + branches: [ "develop", "main" ] + pull_request: + branches: [ "develop" ] + schedule: + - cron: "43 0 * * 5" + +jobs: + analyze: + name: Analyze + runs-on: ubuntu-latest + permissions: + actions: read + contents: read + security-events: write + + strategy: + fail-fast: false + matrix: + language: [ python ] + + steps: + - name: Checkout + uses: actions/checkout@v3 + + - name: Initialize CodeQL + uses: github/codeql-action/init@v2 + with: + languages: ${{ matrix.language }} + queries: +security-and-quality + + - name: Autobuild + uses: github/codeql-action/autobuild@v2 + + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v2 + with: + category: "/language:${{ matrix.language }}" From b976ea08ce691083a3b5d64edea6411c95bafe82 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=B6ren=20Wacker?= <3391614+sorenwacker@users.noreply.github.com> Date: Tue, 19 Sep 2023 01:56:09 -0600 Subject: [PATCH 2/6] Update MaxquantRunner.py --- lrg_omics/proteomics/maxquant/MaxquantRunner.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/lrg_omics/proteomics/maxquant/MaxquantRunner.py b/lrg_omics/proteomics/maxquant/MaxquantRunner.py index 7d79d0c..3459b5f 100644 --- a/lrg_omics/proteomics/maxquant/MaxquantRunner.py +++ b/lrg_omics/proteomics/maxquant/MaxquantRunner.py @@ -24,6 +24,7 @@ def __init__( cleanup=False, verbose=False, output_dir=None, + time='5:00:00', ): """ Runs MaxQuant jobs using a mqpar.txt template, @@ -51,6 +52,7 @@ def __init__( cleanup: bool, default=False * True: removes the files in the run directory when run finishes * False: keep the run files, e.g. for debugging + time: str, default='5:00:00' """ if output_dir is not None: @@ -65,9 +67,11 @@ def __init__( self._tgt_dir = P(out_dir) if isinstance(out_dir, str) else out_dir self._add_raw_name_to_outdir = add_raw_name_to_outdir self._add_uuid_to_rundir = add_uuid_to_rundir - + self._time = time + if sbatch_cmds is None: sbatch_cmds = "" + self._sbatch_cmds = [i.strip() for i in sbatch_cmds.split(";")] self._cleanup = cleanup self._verbose = verbose @@ -93,6 +97,7 @@ def run( submit=False, run=True, with_time=True, + time='5:00:00' ): """ Executes MaxQuant run or only prepares output and run directories. @@ -125,10 +130,11 @@ def run( tgt_dir = abspath(join(os.getcwd(), "out")) else: tgt_dir = abspath(self._tgt_dir) - if self._add_raw_name_to_outdir: tgt_dir = join(tgt_dir, raw_label) - + if self._time: + time = self._time + run_id = f"{raw_label}" if self._add_uuid_to_rundir: @@ -208,6 +214,7 @@ def run( submit=submit, maxquantcmd=self._mqcmd, rundir=run_dir, + time=time ) cmds = "; ".join(cmds) @@ -226,11 +233,12 @@ def gen_sbatch_file( fn="run.sbatch", cold_run=False, maxquantcmd="maxqant", + time='5:00:00', rundir=None, ): cmds_txt = "\n\n".join(commands) txt = f"""#!/bin/bash -#SBATCH --time=5:00:00 +#SBATCH --time={time} #SBATCH --ntasks-per-node=1 #SBATCH --nodes=1 #SBATCH --mem=5000 From 3d62ec0147a323b6c28d6a5df5f0e1cfe3ab4d04 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=B6ren=20Wacker?= <3391614+sorenwacker@users.noreply.github.com> Date: Tue, 19 Sep 2023 02:14:34 -0600 Subject: [PATCH 3/6] Added time argument to lrg_run_maxquant.py --- scripts/lrg_run_maxquant.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/scripts/lrg_run_maxquant.py b/scripts/lrg_run_maxquant.py index 8b864e8..8b7d1b3 100755 --- a/scripts/lrg_run_maxquant.py +++ b/scripts/lrg_run_maxquant.py @@ -67,6 +67,8 @@ help="Remove run directory after running MaxQuant", ) parser.add_argument("--verbose", action="store_true") + parser.add_argument("--time", default='5:00:00') + args = parser.parse_args() mq = MaxquantRunner( @@ -80,6 +82,7 @@ cleanup=args.cleanup, add_raw_name_to_outdir=args.add_raw_name_to_outdir, add_uuid_to_rundir=args.add_uuid_to_rundir, + time=args.time ) for raw_file in args.raw[0]: From 000790cfe3d7edfd2e4ede8db7d0f0989b2039d3 Mon Sep 17 00:00:00 2001 From: Soren Wacker Date: Wed, 20 Sep 2023 12:37:46 -0600 Subject: [PATCH 4/6] .. --- .dvcignore | 0 README.md | 0 lrg_omics/__init__.py | 0 lrg_omics/proteomics/__init__.py | 0 lrg_omics/proteomics/maxquant/MaxquantRunner.py | 16 +++++++++------- scripts/lrg_fake_maxquant.sh | 0 scripts/lrg_get_maxquant_qc_data_from_path.py | 0 scripts/lrg_get_rawtools_qc_data_from_path.py | 0 .../lrg_metabolomics_metadata_from_worklist.py | 0 scripts/lrg_mzML2mzMLb.py | 0 scripts/lrg_run_maxquant.py | 4 ++-- scripts/lrg_thermo_worklist_parser.py | 0 scripts/lrg_upload_raw_file_to_qc_pipeline.py | 0 setup.cfg | 0 setup.py | 0 tests/__init__.py | 0 16 files changed, 11 insertions(+), 9 deletions(-) mode change 100755 => 100644 .dvcignore mode change 100755 => 100644 README.md mode change 100755 => 100644 lrg_omics/__init__.py mode change 100755 => 100644 lrg_omics/proteomics/__init__.py mode change 100755 => 100644 scripts/lrg_fake_maxquant.sh mode change 100755 => 100644 scripts/lrg_get_maxquant_qc_data_from_path.py mode change 100755 => 100644 scripts/lrg_get_rawtools_qc_data_from_path.py mode change 100755 => 100644 scripts/lrg_metabolomics_metadata_from_worklist.py mode change 100755 => 100644 scripts/lrg_mzML2mzMLb.py mode change 100755 => 100644 scripts/lrg_run_maxquant.py mode change 100755 => 100644 scripts/lrg_thermo_worklist_parser.py mode change 100755 => 100644 scripts/lrg_upload_raw_file_to_qc_pipeline.py mode change 100755 => 100644 setup.cfg mode change 100755 => 100644 setup.py mode change 100755 => 100644 tests/__init__.py diff --git a/.dvcignore b/.dvcignore old mode 100755 new mode 100644 diff --git a/README.md b/README.md old mode 100755 new mode 100644 diff --git a/lrg_omics/__init__.py b/lrg_omics/__init__.py old mode 100755 new mode 100644 diff --git a/lrg_omics/proteomics/__init__.py b/lrg_omics/proteomics/__init__.py old mode 100755 new mode 100644 diff --git a/lrg_omics/proteomics/maxquant/MaxquantRunner.py b/lrg_omics/proteomics/maxquant/MaxquantRunner.py index 3459b5f..0ad08ef 100644 --- a/lrg_omics/proteomics/maxquant/MaxquantRunner.py +++ b/lrg_omics/proteomics/maxquant/MaxquantRunner.py @@ -24,7 +24,7 @@ def __init__( cleanup=False, verbose=False, output_dir=None, - time='5:00:00', + runtime='10:00:00', ): """ Runs MaxQuant jobs using a mqpar.txt template, @@ -97,7 +97,7 @@ def run( submit=False, run=True, with_time=True, - time='5:00:00' + runtime=None, ): """ Executes MaxQuant run or only prepares output and run directories. @@ -132,8 +132,8 @@ def run( tgt_dir = abspath(self._tgt_dir) if self._add_raw_name_to_outdir: tgt_dir = join(tgt_dir, raw_label) - if self._time: - time = self._time + if runtime is None: + runtime = self._runtime run_id = f"{raw_label}" @@ -179,6 +179,8 @@ def run( f"if [ ! -d {run_dir}/combined/txt ]; then mkdir {run_dir}/combined/txt ; fi", f"cp time.txt maxquant.err maxquant.out {run_mqpar} {run_dir}/combined/txt/", f"mv {run_dir}/combined/txt/* {tgt_dir}", + f"rm -rf {run_dir}/combined", + f"rm -rf {run_dir}/{raw_label}" ] if self._cleanup: @@ -214,7 +216,7 @@ def run( submit=submit, maxquantcmd=self._mqcmd, rundir=run_dir, - time=time + runtime=runtime ) cmds = "; ".join(cmds) @@ -233,12 +235,12 @@ def gen_sbatch_file( fn="run.sbatch", cold_run=False, maxquantcmd="maxqant", - time='5:00:00', rundir=None, + runtime="10:00:00" ): cmds_txt = "\n\n".join(commands) txt = f"""#!/bin/bash -#SBATCH --time={time} +#SBATCH --time={runtime} #SBATCH --ntasks-per-node=1 #SBATCH --nodes=1 #SBATCH --mem=5000 diff --git a/scripts/lrg_fake_maxquant.sh b/scripts/lrg_fake_maxquant.sh old mode 100755 new mode 100644 diff --git a/scripts/lrg_get_maxquant_qc_data_from_path.py b/scripts/lrg_get_maxquant_qc_data_from_path.py old mode 100755 new mode 100644 diff --git a/scripts/lrg_get_rawtools_qc_data_from_path.py b/scripts/lrg_get_rawtools_qc_data_from_path.py old mode 100755 new mode 100644 diff --git a/scripts/lrg_metabolomics_metadata_from_worklist.py b/scripts/lrg_metabolomics_metadata_from_worklist.py old mode 100755 new mode 100644 diff --git a/scripts/lrg_mzML2mzMLb.py b/scripts/lrg_mzML2mzMLb.py old mode 100755 new mode 100644 diff --git a/scripts/lrg_run_maxquant.py b/scripts/lrg_run_maxquant.py old mode 100755 new mode 100644 index 8b7d1b3..5240a1a --- a/scripts/lrg_run_maxquant.py +++ b/scripts/lrg_run_maxquant.py @@ -67,7 +67,7 @@ help="Remove run directory after running MaxQuant", ) parser.add_argument("--verbose", action="store_true") - parser.add_argument("--time", default='5:00:00') + parser.add_argument("--runtime", default='10:00:00') args = parser.parse_args() @@ -82,7 +82,7 @@ cleanup=args.cleanup, add_raw_name_to_outdir=args.add_raw_name_to_outdir, add_uuid_to_rundir=args.add_uuid_to_rundir, - time=args.time + runtime=args.runtime ) for raw_file in args.raw[0]: diff --git a/scripts/lrg_thermo_worklist_parser.py b/scripts/lrg_thermo_worklist_parser.py old mode 100755 new mode 100644 diff --git a/scripts/lrg_upload_raw_file_to_qc_pipeline.py b/scripts/lrg_upload_raw_file_to_qc_pipeline.py old mode 100755 new mode 100644 diff --git a/setup.cfg b/setup.cfg old mode 100755 new mode 100644 diff --git a/setup.py b/setup.py old mode 100755 new mode 100644 diff --git a/tests/__init__.py b/tests/__init__.py old mode 100755 new mode 100644 From f0c65e35aef772e027f9cb06db0fb39b8aa775bf Mon Sep 17 00:00:00 2001 From: Soren Wacker Date: Wed, 20 Sep 2023 12:59:36 -0600 Subject: [PATCH 5/6] fixed --- lrg_omics/proteomics/maxquant/MaxquantRunner.py | 2 +- tests/proteomics/test__MaxquantRunner.py | 2 -- tests/proteomics/test__lrg_run_maxquant.py | 2 +- 3 files changed, 2 insertions(+), 4 deletions(-) diff --git a/lrg_omics/proteomics/maxquant/MaxquantRunner.py b/lrg_omics/proteomics/maxquant/MaxquantRunner.py index 0ad08ef..e0db6ce 100644 --- a/lrg_omics/proteomics/maxquant/MaxquantRunner.py +++ b/lrg_omics/proteomics/maxquant/MaxquantRunner.py @@ -67,7 +67,7 @@ def __init__( self._tgt_dir = P(out_dir) if isinstance(out_dir, str) else out_dir self._add_raw_name_to_outdir = add_raw_name_to_outdir self._add_uuid_to_rundir = add_uuid_to_rundir - self._time = time + self._runtime = runtime if sbatch_cmds is None: sbatch_cmds = "" diff --git a/tests/proteomics/test__MaxquantRunner.py b/tests/proteomics/test__MaxquantRunner.py index b59aa57..0cd0c66 100644 --- a/tests/proteomics/test__MaxquantRunner.py +++ b/tests/proteomics/test__MaxquantRunner.py @@ -40,10 +40,8 @@ def test_missing_Maxquantcmd_raises_exception(self, tmpdir): del mq def test_input_files_created(self, tmpdir): - run_dir = P(tmpdir) / "run" out_dir = P(tmpdir) / "out" - fn_raw = PATH / "fake" / "fake.raw" fn_mqp = PATH / "maxquant" / "tmt11" / "mqpar" / "mqpar.xml" fn_faa = PATH / "fasta" / "minimal.faa" diff --git a/tests/proteomics/test__lrg_run_maxquant.py b/tests/proteomics/test__lrg_run_maxquant.py index 58f805c..164b5ca 100644 --- a/tests/proteomics/test__lrg_run_maxquant.py +++ b/tests/proteomics/test__lrg_run_maxquant.py @@ -19,12 +19,12 @@ def test__time(tmpdir): def test__missing_faa_raises_exception(tmpdir): - fn_raw = PATH / "fake" / "fake.raw" fn_mqp = PATH / "maxquant" / "tmt11" / "mqpar" / "mqpar.xml" fn_faa = PATH / "fasta" / "minimal.faa" run_dir = P(tmpdir) / "run" out_dir = P(tmpdir) / "out" + cmd = ( f"lrg_run_maxquant.py --fasta {fn_faa} --raw {fn_raw} --mqpar {fn_mqp}" f" --run-dir {run_dir} --out-dir {out_dir}" From 0c3b66dbbd674a8f8ae71282f33b2c9635ead8fa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=B6ren=20Wacker?= <3391614+sorenwacker@users.noreply.github.com> Date: Fri, 6 Oct 2023 09:24:21 +0200 Subject: [PATCH 6/6] Update LICENSE --- LICENSE | 221 ++++++++++++++++++++++++++++++++++++++++++++++++++------ 1 file changed, 200 insertions(+), 21 deletions(-) diff --git a/LICENSE b/LICENSE index cd5120d..ef18dd7 100644 --- a/LICENSE +++ b/LICENSE @@ -1,21 +1,200 @@ - MIT License - -Copyright (c) 2021 - Lewis Research Group (LRG) codebase for omics integration - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. \ No newline at end of file + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [2022] [Lewis Research Group] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License.