diff --git a/.github/workflows/github_draft_release.yml b/.github/workflows/github_draft_release.yml new file mode 100644 index 0000000..14a1838 --- /dev/null +++ b/.github/workflows/github_draft_release.yml @@ -0,0 +1,114 @@ +name: Create GitHub Draft Releases + +on: + workflow_dispatch: + +jobs: + Current_Version: + runs-on: ubuntu-latest + outputs: + version: ${{ steps.master_Current_Version.outputs.version }} + steps: + - name: Checkout code + uses: actions/checkout@v2 + - name: Get current version + id: master_Current_Version + run: | + current_version=$(grep "__version__" alphamap/__init__.py | cut -f3 -d ' ' | sed 's/"//g') + echo "version=$current_version" >> $GITHUB_OUTPUT + + Create_Draft_On_GitHub: + runs-on: ubuntu-latest + needs: Current_Version + outputs: + upload_url: ${{ steps.draft_release.outputs.upload_url }} + steps: + - name: Create Draft Release + id: draft_release + uses: actions/create-release@v1 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + tag_name: v${{ needs.Current_Version.outputs.version }} + release_name: Release version ${{ needs.Current_Version.outputs.version }} + draft: true + prerelease: false + - name: Move release to hidden folder + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: | + release_id=$(curl -s -H "Authorization: token $GITHUB_TOKEN" \ + "https://api.github.com/repos/${{ github.repository }}/releases/tags/v${{ needs.Current_Version.outputs.version }}" \ + | jq -r .id) + curl -X PATCH -H "Authorization: token $GITHUB_TOKEN" \ + -H "Accept: application/vnd.github.v3+json" \ + "https://api.github.com/repos/${{ github.repository }}/releases/$release_id" \ + -d '{"draft": true, "name": ".hidden/v${{ needs.Current_Version.outputs.version }}"}' + Create_MacOS_Release: + runs-on: macos-latest + needs: Create_Draft_On_GitHub + steps: + - name: Checkout code + uses: actions/checkout@v2 + - uses: conda-incubator/setup-miniconda@v2 + with: + auto-update-conda: true + python-version: ${{ matrix.python-version }} + miniconda-version: "latest" + - name: Conda info + shell: bash -l {0} + run: conda info + - name: Creating installer for MacOS + shell: bash -l {0} + run: | + cd misc/one_click_macos + . ./create_installer_macos.sh + - name: Test installer for MacOS + shell: bash -l {0} + run: | + sudo installer -pkg misc/one_click_macos/dist/alphamap_gui_installer_macos.pkg -target / + - name: Upload MacOS Installer + id: upload-release-asset + uses: actions/upload-release-asset@v1 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }} + asset_path: misc/one_click_macos/dist/alphamap_gui_installer_macos.pkg + asset_name: alphamap_gui_installer_macos.pkg + asset_content_type: application/octet-stream + Create_Windows_Release: + runs-on: windows-latest + needs: Create_Draft_On_GitHub + steps: + - name: Checkout code + uses: actions/checkout@v2 + - uses: conda-incubator/setup-miniconda@v2 + with: + auto-update-conda: true + python-version: ${{ matrix.python-version }} + - name: Conda info + shell: bash -l {0} + run: conda info + - name: Creating installer for Windows + shell: bash -l {0} + run: | + cd misc/one_click_windows + . ./create_installer_windows.sh + - name: Test installer for Windows + shell: bash -l {0} + run: | + cd misc/one_click_windows/dist/ + echo "TODO, this test seems to freeze the runner..." + # ./alphamap_gui_installer_windows.exe //verysilent //log=log.txt //noicons //tasks= //portable=1 + # cat log.txt + - name: Upload Windows Installer + id: upload-release-asset + uses: actions/upload-release-asset@v1 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }} + asset_path: misc/one_click_windows/dist/alphamap_installer_windows.exe + asset_name: alphamap_installer_windows.exe + asset_content_type: application/octet-stream \ No newline at end of file diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml deleted file mode 100644 index f7cbcdc..0000000 --- a/.github/workflows/main.yml +++ /dev/null @@ -1,42 +0,0 @@ -name: CI -on: - push: - branches: [ master ] - pull_request: - branches: [ master, develop ] - workflow_dispatch: -jobs: - build: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v1 - - uses: actions/setup-python@v1 - with: - python-version: '3.8' - architecture: 'x64' - - name: Install the library - run: | - pip install nbdev==1.2.5 jupyter - pip install -e . - - name: Read all notebooks - run: | - nbdev_read_nbs - - name: Check if all notebooks are cleaned - run: | - echo "Check we are starting with clean git checkout" - if [ -n "$(git status -uno -s)" ]; then echo "git status is not clean"; false; fi - echo "Trying to strip out notebooks" - nbdev_clean_nbs - echo "Check that strip out was unnecessary" - git status -s # display the status to see which nbs need cleaning up - if [ -n "$(git status -uno -s)" ]; then echo -e "!!! Detected unstripped out notebooks\n!!!Remember to run nbdev_install_git_hooks"; false; fi - - name: Check if there is no diff library/notebooks - run: | - if [ -n "$(nbdev_diff_nbs)" ]; then echo -e "!!! Detected difference between the notebooks and the library"; false; fi - - name: Run notebook tests - run: | - nbdev_test_nbs - - name: Run system test - run: | - mv testdata nbs/testdata - nbdev_test_nbs --fname Workflow.ipynb diff --git a/README.md b/README.md index 69b1778..2aff888 100644 --- a/README.md +++ b/README.md @@ -37,6 +37,11 @@ The GUI of AlphaMap is a completely stand-alone tool that requires no knowledge AlphaMap can be installed in an existing Python 3.8 environment with a single `bash` command. *This `bash` command can also be run directly from within a Jupyter notebook by prepending it with a `!`*. +```bash +pip install alphamap[stable] +``` +The [stable] tag ensures you get the latest stable release with fixed dependencies. However, it can be omitted if you prefer more flexible dependency versions: + ```bash pip install alphamap ``` @@ -44,7 +49,7 @@ pip install alphamap When a new version of AlphaMap becomes available, the old version can easily be upgraded by running e.g. the command again with an additional `--upgrade` flag: ```bash -pip install alphamap --upgrade +pip install --upgrade alphamap[stable] ``` NOTE: When installing with `pip`, UniProt information is not included. Upon first usage of a specific Organism, its information will be automatically downloaded from UniProt. @@ -71,11 +76,13 @@ For any Python package, it is highly recommended to use a [conda virtual environ ```bash conda create -n alphamap python=3.8 -y conda activate alphamap -pip install -e . +pip install -e ".[stable]" ``` * By using the editable flag `-e`, all modifications to the AlphaMap [source code folder](alphamap) are directly reflected when running AlphaMap. Note that the AlphaMap folder cannot be moved and/or renamed if an editable version is installed. +* The [stable] tag ensures you get the latest stable release with fixed dependencies. However, it can be omitted if you prefer more flexible dependency versions. + * When using Jupyter notebooks and multiple conda environments direcly from the terminal, it is recommended to `conda install nb_conda_kernels` in the conda base environment. Hereafter, running a `jupyter notebook` from the conda base environment should have a `python [conda env: alphamap]` kernel available, in addition to all other conda kernels in which the command `conda install ipykernel` was run. diff --git a/Workflow.ipynb b/Workflow.ipynb index 71a8ca2..03c8c7a 100644 --- a/Workflow.ipynb +++ b/Workflow.ipynb @@ -7974,9 +7974,9 @@ } }, "text/html": [ - "
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" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "outputs": [], "source": [ "#hide\n", "plot_peptide_traces(formatted_diann_data,\n", @@ -61773,7 +1325,7 @@ }, { "cell_type": "code", - "execution_count": 32, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -61791,7 +1343,7 @@ }, { "cell_type": "code", - "execution_count": 33, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -61899,7 +1451,7 @@ }, { "cell_type": "code", - "execution_count": 34, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -62023,7 +1575,7 @@ }, { "cell_type": "code", - "execution_count": 35, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -62042,7 +1594,7 @@ }, { "cell_type": "code", - "execution_count": 36, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -62104,10 +1656,13 @@ " os.remove(new_file)\n", " except:\n", " pass\n", - " shutil.copyfile(src = 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handle_kernel_cleanup);\n\n OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n safe: true,\n index: 0\n });\n}\n\nif (window.Jupyter !== undefined) {\n try {\n var events = require('base/js/events');\n var OutputArea = require('notebook/js/outputarea').OutputArea;\n if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n } catch(err) {\n }\n}\n" - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "outputs": [], "source": [ "#export\n", "import os\n", @@ -62579,14 +1747,14 @@ }, { "cell_type": "code", - "execution_count": 39, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# #hide\n", "# mod_html, js_path, cif_path = plot_3d_structure(df = formatted_diann_data,\n", "# name = 'proteome',\n", - "# protein = \"P23284\", #Q9H7C9, P23284\n", + "# protein = \"P23284\", #Q9H7C9, P23284 ## not working example: Q15149\n", "# fasta = human_fasta,\n", "# selected_coloring = 'AlphaFold quality', #'AlphaFold exposure', #'AlphaFold quality', 'MS data'\n", "# dashboard = False)\n", @@ -62596,7 +1764,7 @@ }, { "cell_type": "code", - "execution_count": 40, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -62612,7 +1780,7 @@ }, { "cell_type": "code", - "execution_count": 41, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -62661,7 +1829,7 @@ }, { "cell_type": "code", - "execution_count": 42, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -62748,7 +1916,7 @@ }, { "cell_type": "code", - "execution_count": 43, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -62770,7 +1938,7 @@ }, { "cell_type": "code", - "execution_count": 44, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -62791,7 +1959,7 @@ }, { "cell_type": "code", - "execution_count": 45, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -62802,7 +1970,7 @@ }, { "cell_type": "code", - "execution_count": 46, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -62812,23 +1980,9 @@ }, { "cell_type": "code", - "execution_count": 47, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Converted Importing.ipynb.\n", - "Converted Preprocessing.ipynb.\n", - "Converted SequencePlot.ipynb.\n", - "Converted Uniprot_integration.ipynb.\n", - "Converted index.ipynb.\n", - "Converted organisms_data.ipynb.\n", - "Converted proteolytic_cleavage.ipynb.\n" - ] - } - ], + "outputs": [], "source": [ "#hide\n", "from nbdev.export import *\n", diff --git a/nbs/Uniprot_integration.ipynb b/nbs/Uniprot_integration.ipynb index 4415765..2043baf 100644 --- a/nbs/Uniprot_integration.ipynb +++ b/nbs/Uniprot_integration.ipynb @@ -477,21 +477,7 @@ "cell_type": "code", "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Converted Importing.ipynb.\n", - "Converted Preprocessing.ipynb.\n", - "Converted SequencePlot.ipynb.\n", - "Converted Uniprot_integration.ipynb.\n", - "Converted index.ipynb.\n", - "Converted organisms_data.ipynb.\n", - "Converted proteolytic_cleavage.ipynb.\n" - ] - } - ], + "outputs": [], "source": [ "#hide\n", "from nbdev.export import *\n", diff --git a/nbs/index.ipynb b/nbs/index.ipynb index d13a420..efeed46 100644 --- a/nbs/index.ipynb +++ b/nbs/index.ipynb @@ -183,21 +183,7 @@ "cell_type": "code", "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Converted Importing.ipynb.\n", - "Converted Preprocessing.ipynb.\n", - "Converted SequencePlot.ipynb.\n", - "Converted Uniprot_integration.ipynb.\n", - "Converted index.ipynb.\n", - "Converted organisms_data.ipynb.\n", - "Converted proteolytic_cleavage.ipynb.\n" - ] - } - ], + "outputs": [], "source": [ "#hide\n", "from nbdev.export import *\n", diff --git a/nbs/organisms_data.ipynb b/nbs/organisms_data.ipynb index 13e3da3..cb0add0 100644 --- a/nbs/organisms_data.ipynb +++ b/nbs/organisms_data.ipynb @@ -90,19 +90,7 @@ "cell_type": "code", "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'fasta_name': 'rat_[10116].fasta',\n", - " 'uniprot_name': 'preprocessed_uniprot_rat.csv'}" - ] - }, - "execution_count": null, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "all_organisms['Rat']" ] @@ -293,21 +281,7 @@ "cell_type": "code", "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Converted Importing.ipynb.\n", - "Converted Preprocessing.ipynb.\n", - "Converted SequencePlot.ipynb.\n", - "Converted Uniprot_integration.ipynb.\n", - "Converted index.ipynb.\n", - "Converted organisms_data.ipynb.\n", - "Converted proteolytic_cleavage.ipynb.\n" - ] - } - ], + "outputs": [], "source": [ "#hide\n", "from nbdev.export import *\n", @@ -324,9 +298,21 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python [conda env:alphamap] *", "language": "python", - "name": "python3" + "name": "conda-env-alphamap-py" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.18" } }, "nbformat": 4, diff --git a/nbs/proteolytic_cleavage.ipynb b/nbs/proteolytic_cleavage.ipynb index 1bab0e4..31e41a8 100644 --- a/nbs/proteolytic_cleavage.ipynb +++ b/nbs/proteolytic_cleavage.ipynb @@ -84,18 +84,7 @@ "cell_type": "code", "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'([KR](?=[^P]))'" - ] - }, - "execution_count": null, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "protease_dict[\"trypsin\"]" ] @@ -195,21 +184,7 @@ "cell_type": "code", "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Converted Importing.ipynb.\n", - "Converted Preprocessing.ipynb.\n", - "Converted SequencePlot.ipynb.\n", - "Converted Uniprot_integration.ipynb.\n", - "Converted index.ipynb.\n", - "Converted organisms_data.ipynb.\n", - "Converted proteolytic_cleavage.ipynb.\n" - ] - } - ], + "outputs": [], "source": [ "#hide\n", "from nbdev.export import *\n", diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..912bed6 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,80 @@ +[build-system] +requires = ["setuptools"] +build-backend = "setuptools.build_meta" + +[project] +name = "alphamap" +requires-python = ">=3.8.0" +dynamic = ["version", "dependencies", "optional-dependencies"] + +authors = [ + {name = "Isabell Bludau, Eugenia Voytik", email = "bludau@biochem.mpg.de"} +] + +readme = "README.md" +keywords = [ + "mass spectrometry", + "proteomics", + "search engine", + "DIA", + "data-independent acquisition", + "bioinformatics", + "AlphaPept", + "AlphaPept ecosystem", +] +license = {file = "LICENSE.txt"} +classifiers = [ + "Development Status :: 4 - Beta", + # "Development Status :: 5 - Production/Stable", + # "Development Status :: 6 - Mature", + # "Development Status :: 7 - Inactive" + "Intended Audience :: Science/Research", + "License :: OSI Approved :: Apache Software License", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Topic :: Scientific/Engineering :: Bio-Informatics", +] + +[project.urls] + +"Paper preprint" = "https://www.biochem.mpg.de/mann" +Repository = "https://github.com/MannLabs/alphamap" +#Documentation = "https://readthedocs.org" +#Changelog = "https://github.com/me/spam/blob/master/CHANGELOG.md" +Issues = "https://github.com/MannLabs/alphamap/issues" +"Mann Labs Homepage" = "https://www.biochem.mpg.de/mann" + +[tool.setuptools.packages] +find = {} + +[tool.setuptools.dynamic] +# https://stackoverflow.com/a/73600610 +dependencies = {file = ["requirements_loose.txt"]} +optional-dependencies = { stable = { file = ["requirements_stable.txt"] }} +version = {attr = "alphamap.__version__"} + +[project.scripts] +alphamap = "alphamap.gui:run" + + +[tool.ruff.lint] +select = [ + # pycodestyle + "E", + # Pyflakes + "F", + # pyupgrade + "UP", + # flake8-bugbear + "B", + # flake8-simplify + "SIM", + # isort + "I", +] + +ignore = [ + "E501", # Line too long (ruff wraps code, but not docstrings) + "B028", # No explicit `stacklevel` keyword argument found (for warnings) + "B905" # This causes problems in numba code: `zip()` without an explicit `strict=` parameter +] \ No newline at end of file diff --git a/requirements_loose.txt b/requirements_loose.txt new file mode 100644 index 0000000..c5c7d10 --- /dev/null +++ b/requirements_loose.txt @@ -0,0 +1,13 @@ +numpy +pandas +panel +param +plotly +pyteomics +pdfrw +psutil +reportlab +kaleido +bokeh +structuremap +h5py \ No newline at end of file diff --git a/requirements.txt b/requirements_stable.txt similarity index 73% rename from requirements.txt rename to requirements_stable.txt index 0da1af9..a9f2e66 100644 --- a/requirements.txt +++ b/requirements_stable.txt @@ -1,4 +1,4 @@ -numpy==1.19.2 +numpy==1.24.4 pandas==1.4.0 panel==0.10.3 param==1.10.0 @@ -10,4 +10,6 @@ reportlab==3.5.59 kaleido==0.2.1 bokeh==2.2.2 structuremap==0.0.8 -h5py==3.6.0 +h5py==3.7.0 +jinja2==2.11.3 +markupsafe==2.0.1 \ No newline at end of file diff --git a/settings.ini b/settings.ini index f3022df..fe0b715 100644 --- a/settings.ini +++ b/settings.ini @@ -13,7 +13,7 @@ user = ibludau # author_email = email@example.com copyright = Mann Labs branch = master -version = 0.1.10 +version = 0.1.11 min_python = 3.8 audience = Developers language = English diff --git a/setup.py b/setup.py deleted file mode 100644 index 187e717..0000000 --- a/setup.py +++ /dev/null @@ -1,54 +0,0 @@ -from pkg_resources import parse_version -from configparser import ConfigParser -import setuptools -assert parse_version(setuptools.__version__)>=parse_version('36.2') - -# note: all settings are in settings.ini; edit there, not here -config = ConfigParser(delimiters=['=']) -config.read('settings.ini') -cfg = config['DEFAULT'] - -cfg_keys = 'version description keywords author author_email'.split() -expected = cfg_keys + "lib_name user branch license status min_python audience language".split() -for o in expected: assert o in cfg, "missing expected setting: {}".format(o) -setup_cfg = {o:cfg[o] for o in cfg_keys} - -licenses = { - 'apache2': ('Apache Software License 2.0','OSI Approved :: Apache Software License'), -} -statuses = [ '1 - Planning', '2 - Pre-Alpha', '3 - Alpha', - '4 - Beta', '5 - Production/Stable', '6 - Mature', '7 - Inactive' ] -py_versions = '2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8'.split() - -#requirements = cfg.get('requirements','').split() -with open("requirements.txt") as requirements_file: - requirements = [] - for line in requirements_file: - # TODO, this should be a proper regex parsing - # requirement, version = line.split("==") - # requirements.append(requirement) - requirements.append(line) - -lic = licenses[cfg['license']] -min_python = cfg['min_python'] - -setuptools.setup( - name = cfg['lib_name'], - license = lic[0], - classifiers = [ - 'Development Status :: ' + statuses[int(cfg['status'])], - 'Intended Audience :: ' + cfg['audience'].title(), - 'License :: ' + lic[1], - 'Natural Language :: ' + cfg['language'].title(), - ] + ['Programming Language :: Python :: '+o for o in py_versions[py_versions.index(min_python):]], - url = cfg['git_url'], - packages = setuptools.find_packages(), - include_package_data = True, - install_requires = requirements, - dependency_links = cfg.get('dep_links','').split(), - python_requires = '>=' + cfg['min_python'], - long_description = open('README.md').read(), - long_description_content_type = 'text/markdown', - zip_safe = False, - entry_points = { 'console_scripts': cfg.get('console_scripts','').split() }, - **setup_cfg)