Metadata-Version: 2.4
Name: fhr
Version: 0.6.0
Summary: Renamed to fair-bioheaders: installing fhr installs fair-bioheaders
Author-email: David Molik <david.molik@usda.gov>, Adam Wright <adam.wright@oicr.on.ca>
License: FAIR-bioHeaders-Tools
        LICENSE AND HISTORICAL PUBLIC-DOMAIN NOTICE
        
        1. Scope and transition
        
        This repository contains historical USDA Agricultural Research Service
        (USDA-ARS) public-domain material and subsequent project contributions
        licensed under the Mozilla Public License, version 2.0 (MPL-2.0).
        
        David Molik left USDA in February 2025. The project's licensing policy is
        MPL-2.0 for new project contributions from March 2025 onward, including
        applicable additions and modifications to existing material. This policy
        covers project code, specifications, schemas and documentation, subject
        to the historical and third-party exceptions described here.
        
        Historical USDA-ARS material released under the public-domain notice below
        remains public domain within the United States. No copyright is claimed in
        that material by this notice, and MPL-2.0 does not withdraw or restrict the
        rights already available in the public-domain portions.
        
        For files containing both historical public-domain material and subsequent
        copyrightable contributions, MPL-2.0 applies to the applicable subsequent
        contributions; it does not make the underlying public-domain material
        exclusively MPL-2.0. File notices and version history identify provenance.
        A file's most recent modification date alone does not determine the status
        of every portion of that file.
        
        Third-party material retains its own applicable licenses and notices.
        Previously distributed versions retain the permissions under which they
        were distributed. This notice does not revoke any previously granted rights.
        
        The historical USDA notice is reproduced verbatim in section 3, including
        its original FAQ and attribution. Its references to government authorship
        apply to the historical USDA material, not to all present-day contributors
        or all material now in this repository.
        
        2. Mozilla Public License 2.0
        
        This Source Code Form is subject to the terms of the Mozilla Public
        License, v. 2.0. If a copy of the MPL was not distributed with this
        file, You can obtain one at https://mozilla.org/MPL/2.0/.
        
        The unmodified license text follows.
        
        Mozilla Public License Version 2.0
        ==================================
        
        1. Definitions
        --------------
        
        1.1. "Contributor"
            means each individual or legal entity that creates, contributes to
            the creation of, or owns Covered Software.
        
        1.2. "Contributor Version"
            means the combination of the Contributions of others (if any) used
            by a Contributor and that particular Contributor's Contribution.
        
        1.3. "Contribution"
            means Covered Software of a particular Contributor.
        
        1.4. "Covered Software"
            means Source Code Form to which the initial Contributor has attached
            the notice in Exhibit A, the Executable Form of such Source Code
            Form, and Modifications of such Source Code Form, in each case
            including portions thereof.
        
        1.5. "Incompatible With Secondary Licenses"
            means
        
            (a) that the initial Contributor has attached the notice described
                in Exhibit B to the Covered Software; or
        
            (b) that the Covered Software was made available under the terms of
                version 1.1 or earlier of the License, but not also under the
                terms of a Secondary License.
        
        1.6. "Executable Form"
            means any form of the work other than Source Code Form.
        
        1.7. "Larger Work"
            means a work that combines Covered Software with other material, in
            a separate file or files, that is not Covered Software.
        
        1.8. "License"
            means this document.
        
        1.9. "Licensable"
            means having the right to grant, to the maximum extent possible,
            whether at the time of the initial grant or subsequently, any and
            all of the rights conveyed by this License.
        
        1.10. "Modifications"
            means any of the following:
        
            (a) any file in Source Code Form that results from an addition to,
                deletion from, or modification of the contents of Covered
                Software; or
        
            (b) any new file in Source Code Form that contains any Covered
                Software.
        
        1.11. "Patent Claims" of a Contributor
            means any patent claim(s), including without limitation, method,
            process, and apparatus claims, in any patent Licensable by such
            Contributor that would be infringed, but for the grant of the
            License, by the making, using, selling, offering for sale, having
            made, import, or transfer of either its Contributions or its
            Contributor Version.
        
        1.12. "Secondary License"
            means either the GNU General Public License, Version 2.0, the GNU
            Lesser General Public License, Version 2.1, the GNU Affero General
            Public License, Version 3.0, or any later versions of those
            licenses.
        
        1.13. "Source Code Form"
            means the form of the work preferred for making modifications.
        
        1.14. "You" (or "Your")
            means an individual or a legal entity exercising rights under this
            License. For legal entities, "You" includes any entity that
            controls, is controlled by, or is under common control with You. For
            purposes of this definition, "control" means (a) the power, direct
            or indirect, to cause the direction or management of such entity,
            whether by contract or otherwise, or (b) ownership of more than
            fifty percent (50%) of the outstanding shares or beneficial
            ownership of such entity.
        
        2. License Grants and Conditions
        --------------------------------
        
        2.1. Grants
        
        Each Contributor hereby grants You a world-wide, royalty-free,
        non-exclusive license:
        
        (a) under intellectual property rights (other than patent or trademark)
            Licensable by such Contributor to use, reproduce, make available,
            modify, display, perform, distribute, and otherwise exploit its
            Contributions, either on an unmodified basis, with Modifications, or
            as part of a Larger Work; and
        
        (b) under Patent Claims of such Contributor to make, use, sell, offer
            for sale, have made, import, and otherwise transfer either its
            Contributions or its Contributor Version.
        
        2.2. Effective Date
        
        The licenses granted in Section 2.1 with respect to any Contribution
        become effective for each Contribution on the date the Contributor first
        distributes such Contribution.
        
        2.3. Limitations on Grant Scope
        
        The licenses granted in this Section 2 are the only rights granted under
        this License. No additional rights or licenses will be implied from the
        distribution or licensing of Covered Software under this License.
        Notwithstanding Section 2.1(b) above, no patent license is granted by a
        Contributor:
        
        (a) for any code that a Contributor has removed from Covered Software;
            or
        
        (b) for infringements caused by: (i) Your and any other third party's
            modifications of Covered Software, or (ii) the combination of its
            Contributions with other software (except as part of its Contributor
            Version); or
        
        (c) under Patent Claims infringed by Covered Software in the absence of
            its Contributions.
        
        This License does not grant any rights in the trademarks, service marks,
        or logos of any Contributor (except as may be necessary to comply with
        the notice requirements in Section 3.4).
        
        2.4. Subsequent Licenses
        
        No Contributor makes additional grants as a result of Your choice to
        distribute the Covered Software under a subsequent version of this
        License (see Section 10.2) or under the terms of a Secondary License (if
        permitted under the terms of Section 3.3).
        
        2.5. Representation
        
        Each Contributor represents that the Contributor believes its
        Contributions are its original creation(s) or it has sufficient rights
        to grant the rights to its Contributions conveyed by this License.
        
        2.6. Fair Use
        
        This License is not intended to limit any rights You have under
        applicable copyright doctrines of fair use, fair dealing, or other
        equivalents.
        
        2.7. Conditions
        
        Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
        in Section 2.1.
        
        3. Responsibilities
        -------------------
        
        3.1. Distribution of Source Form
        
        All distribution of Covered Software in Source Code Form, including any
        Modifications that You create or to which You contribute, must be under
        the terms of this License. You must inform recipients that the Source
        Code Form of the Covered Software is governed by the terms of this
        License, and how they can obtain a copy of this License. You may not
        attempt to alter or restrict the recipients' rights in the Source Code
        Form.
        
        3.2. Distribution of Executable Form
        
        If You distribute Covered Software in Executable Form then:
        
        (a) such Covered Software must also be made available in Source Code
            Form, as described in Section 3.1, and You must inform recipients of
            the Executable Form how they can obtain a copy of such Source Code
            Form by reasonable means in a timely manner, at a charge no more
            than the cost of distribution to the recipient; and
        
        (b) You may distribute such Executable Form under the terms of this
            License, or sublicense it under different terms, provided that the
            license for the Executable Form does not attempt to limit or alter
            the recipients' rights in the Source Code Form under this License.
        
        3.3. Distribution of a Larger Work
        
        You may create and distribute a Larger Work under terms of Your choice,
        provided that You also comply with the requirements of this License for
        the Covered Software. If the Larger Work is a combination of Covered
        Software with a work governed by one or more Secondary Licenses, and the
        Covered Software is not Incompatible With Secondary Licenses, this
        License permits You to additionally distribute such Covered Software
        under the terms of such Secondary License(s), so that the recipient of
        the Larger Work may, at their option, further distribute the Covered
        Software under the terms of either this License or such Secondary
        License(s).
        
        3.4. Notices
        
        You may not remove or alter the substance of any license notices
        (including copyright notices, patent notices, disclaimers of warranty,
        or limitations of liability) contained within the Source Code Form of
        the Covered Software, except that You may alter any license notices to
        the extent required to remedy known factual inaccuracies.
        
        3.5. Application of Additional Terms
        
        You may choose to offer, and to charge a fee for, warranty, support,
        indemnity or liability obligations to one or more recipients of Covered
        Software. However, You may do so only on Your own behalf, and not on
        behalf of any Contributor. You must make it absolutely clear that any
        such warranty, support, indemnity, or liability obligation is offered by
        You alone, and You hereby agree to indemnify every Contributor for any
        liability incurred by such Contributor as a result of warranty, support,
        indemnity or liability terms You offer. You may include additional
        disclaimers of warranty and limitations of liability specific to any
        jurisdiction.
        
        4. Inability to Comply Due to Statute or Regulation
        ---------------------------------------------------
        
        If it is impossible for You to comply with any of the terms of this
        License with respect to some or all of the Covered Software due to
        statute, judicial order, or regulation then You must: (a) comply with
        the terms of this License to the maximum extent possible; and (b)
        describe the limitations and the code they affect. Such description must
        be placed in a text file included with all distributions of the Covered
        Software under this License. Except to the extent prohibited by statute
        or regulation, such description must be sufficiently detailed for a
        recipient of ordinary skill to be able to understand it.
        
        5. Termination
        --------------
        
        5.1. The rights granted under this License will terminate automatically
        if You fail to comply with any of its terms. However, if You become
        compliant, then the rights granted under this License from a particular
        Contributor are reinstated (a) provisionally, unless and until such
        Contributor explicitly and finally terminates Your grants, and (b) on an
        ongoing basis, if such Contributor fails to notify You of the
        non-compliance by some reasonable means prior to 60 days after You have
        come back into compliance. Moreover, Your grants from a particular
        Contributor are reinstated on an ongoing basis if such Contributor
        notifies You of the non-compliance by some reasonable means, this is the
        first time You have received notice of non-compliance with this License
        from such Contributor, and You become compliant prior to 30 days after
        Your receipt of the notice.
        
        5.2. If You initiate litigation against any entity by asserting a patent
        infringement claim (excluding declaratory judgment actions,
        counter-claims, and cross-claims) alleging that a Contributor Version
        directly or indirectly infringes any patent, then the rights granted to
        You by any and all Contributors for the Covered Software under Section
        2.1 of this License shall terminate.
        
        5.3. In the event of termination under Sections 5.1 or 5.2 above, all
        end user license agreements (excluding distributors and resellers) which
        have been validly granted by You or Your distributors under this License
        prior to termination shall survive termination.
        
        ************************************************************************
        *                                                                      *
        *  6. Disclaimer of Warranty                                           *
        *  -------------------------                                           *
        *                                                                      *
        *  Covered Software is provided under this License on an "as is"       *
        *  basis, without warranty of any kind, either expressed, implied, or  *
        *  statutory, including, without limitation, warranties that the       *
        *  Covered Software is free of defects, merchantable, fit for a        *
        *  particular purpose or non-infringing. The entire risk as to the     *
        *  quality and performance of the Covered Software is with You.        *
        *  Should any Covered Software prove defective in any respect, You     *
        *  (not any Contributor) assume the cost of any necessary servicing,   *
        *  repair, or correction. This disclaimer of warranty constitutes an   *
        *  essential part of this License. No use of any Covered Software is   *
        *  authorized under this License except under this disclaimer.         *
        *                                                                      *
        ************************************************************************
        
        ************************************************************************
        *                                                                      *
        *  7. Limitation of Liability                                          *
        *  --------------------------                                          *
        *                                                                      *
        *  Under no circumstances and under no legal theory, whether tort      *
        *  (including negligence), contract, or otherwise, shall any           *
        *  Contributor, or anyone who distributes Covered Software as          *
        *  permitted above, be liable to You for any direct, indirect,         *
        *  special, incidental, or consequential damages of any character      *
        *  including, without limitation, damages for lost profits, loss of    *
        *  goodwill, work stoppage, computer failure or malfunction, or any    *
        *  and all other commercial damages or losses, even if such party      *
        *  shall have been informed of the possibility of such damages. This   *
        *  limitation of liability shall not apply to liability for death or   *
        *  personal injury resulting from such party's negligence to the       *
        *  extent applicable law prohibits such limitation. Some               *
        *  jurisdictions do not allow the exclusion or limitation of           *
        *  incidental or consequential damages, so this exclusion and          *
        *  limitation may not apply to You.                                    *
        *                                                                      *
        ************************************************************************
        
        8. Litigation
        -------------
        
        Any litigation relating to this License may be brought only in the
        courts of a jurisdiction where the defendant maintains its principal
        place of business and such litigation shall be governed by laws of that
        jurisdiction, without reference to its conflict-of-law provisions.
        Nothing in this Section shall prevent a party's ability to bring
        cross-claims or counter-claims.
        
        9. Miscellaneous
        ----------------
        
        This License represents the complete agreement concerning the subject
        matter hereof. If any provision of this License is held to be
        unenforceable, such provision shall be reformed only to the extent
        necessary to make it enforceable. Any law or regulation which provides
        that the language of a contract shall be construed against the drafter
        shall not be used to construe this License against a Contributor.
        
        10. Versions of the License
        ---------------------------
        
        10.1. New Versions
        
        Mozilla Foundation is the license steward. Except as provided in Section
        10.3, no one other than the license steward has the right to modify or
        publish new versions of this License. Each version will be given a
        distinguishing version number.
        
        10.2. Effect of New Versions
        
        You may distribute the Covered Software under the terms of the version
        of the License under which You originally received the Covered Software,
        or under the terms of any subsequent version published by the license
        steward.
        
        10.3. Modified Versions
        
        If you create software not governed by this License, and you want to
        create a new license for such software, you may create and use a
        modified version of this License if you rename the license and remove
        any references to the name of the license steward (except to note that
        such modified license differs from this License).
        
        10.4. Distributing Source Code Form that is Incompatible With Secondary
        Licenses
        
        If You choose to distribute Source Code Form that is Incompatible With
        Secondary Licenses under the terms of this version of the License, the
        notice described in Exhibit B of this License must be attached.
        
        Exhibit A - Source Code Form License Notice
        -------------------------------------------
        
          This Source Code Form is subject to the terms of the Mozilla Public
          License, v. 2.0. If a copy of the MPL was not distributed with this
          file, You can obtain one at https://mozilla.org/MPL/2.0/.
        
        If it is not possible or desirable to put the notice in a particular
        file, then You may include the notice in a location (such as a LICENSE
        file in a relevant directory) where a recipient would be likely to look
        for such a notice.
        
        You may add additional accurate notices of copyright ownership.
        
        Exhibit B - "Incompatible With Secondary Licenses" Notice
        ---------------------------------------------------------
        
          This Source Code Form is "Incompatible With Secondary Licenses", as
          defined by the Mozilla Public License, v. 2.0.
        
        3. Historical USDA Public Domain Notice (preserved verbatim)
        
        CONTENTS
        
          Public Domain Notice
          Exceptions (for bundled 3rd-party code)
          Copyright F.A.Q.
        
        
        ==============================================================
                             PUBLIC DOMAIN NOTICE
                    United States Department of Agriculture
                         Agricultural Research Service
        
        With the exception of certain third-party files summarized below, this
        software is a "United States Government Work" under the terms of the
        United States Copyright Act.  It was written as part of the authors'
        official duties as United States Government employees and thus cannot
        be copyrighted.  This software is freely available to the public for
        use. The United States Department of Agriculture, Agricultural 
        Research Service (USDA - ARS) and the U.S. Government have not placed 
        any restriction on its use or reproduction.
        
        Although all reasonable efforts have been taken to ensure the accuracy
        and reliability of the software and data, the USDA ARS and the U.S.
        Government do not and cannot warrant the performance or results tha may 
        be obtained by using this software or data. The USDA ARS and the U.S. 
        Government disclaim all warranties, express or implied, including
        warranties of performance, merchantability or fitness for any particular 
        purpose.
        
        Please cite the authors in any work or product based on this material.
        
        
        ==============================================================
        EXCEPTIONS (in all cases excluding USDA-ARS-written makefiles):
        
        Location: 
        Author:   
        License:  
        
        
        ==============================================================
        Copyright F.A.Q.
        
        
        --------------------------------------------------------------
        Q. Our product makes use of the USDA - ARS source code, and we made changes
           and additions to that version of the USDA - ARS code to better fit it to
           our needs. Can we copyright the code, and how?
        
        A. You can copyright only the *changes* or the *additions* you made to the
           NCBI source code. You should identify unambiguously those sections of
           the code that were modified, e.g. by commenting any changes you made
           in the code you distribute. Therefore, your license has to make clear
           to users that your product is a combination of code that is public domain
           within the U.S. (but may be subject to copyright by the U.S. in foreign
           countries) and code that has been created or modified by you.
        
        --------------------------------------------------------------
        Q. Can we (re)license all or part of the USDA - ARS source code?
        
        A. No, you cannot license or relicense the source code written by USDA - ARS
           since you cannot claim any copyright in the software that was developed
           at USDA - ARS as a 'government work' and consequently is in the public 
           domain within the U.S.
        
        --------------------------------------------------------------
        Q. What if these copyright guidelines are not clear enough or are not
           applicable to my particular case?
        
        A. Contact us. Send your questions to 'answers@usda.gov'.
        --------------------------------------------------------------
        
        This file was modified from the NCBI Boilerplate LICENSE file
        
Project-URL: Homepage, https://github.com/FAIR-bioHeaders/FAIR-bioHeaders-Tools
Project-URL: Repository, https://github.com/FAIR-bioHeaders/FAIR-bioHeaders-Tools
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: fair-bioheaders==0.6.0
Dynamic: license-file

# fhr (renamed to fair-bioheaders)

The `fhr` package on PyPI is now
[`fair-bioheaders`](https://pypi.org/project/fair-bioheaders/), developed at
[FAIR-bioHeaders-Tools](https://github.com/FAIR-bioHeaders/FAIR-bioHeaders-Tools).

This `fhr` distribution contains no code. It requires the same version of
`fair-bioheaders`, so `pip install fhr` and `pip install -U fhr` keep installing
the tools. For new installs and requirements, use `fair-bioheaders` directly:

```bash
python -m pip install fair-bioheaders
```

Everything that worked with `fhr` 0.3 keeps working:

- The `fhr-convert`, `fhr-validate`, `fhr-fasta-*`, and `fhr-gfa-*` commands are
  unchanged. The new `bioheaders` command offers the same operations as
  subcommands (`bioheaders convert`, `validate`, `combine`, `strip`, `verify`).
- `import fhr` and `from fhr.cli import ...` still work but emit a
  `DeprecationWarning`; use `import bioheaders` and `bioheaders.cli` instead.

This distribution also declares the `fhr-*` commands, so that upgrading from
`fhr` 0.3 with pip keeps them. If you later uninstall `fhr`, restore them with:

```bash
python -m pip install --force-reinstall --no-deps fair-bioheaders
```

In an environment that still has `fhr` 0.3, uninstall it before installing
`fair-bioheaders` on its own, or upgrade with `python -m pip install -U fhr`.

See the [changelog](https://github.com/FAIR-bioHeaders/FAIR-bioHeaders-Tools/blob/main/CHANGELOG.md)
for details.
