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Oct 1, 2023
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Dependencies #52

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434d61f
update dependencies for 3.11 and documentation
gtluu Sep 29, 2023
31e306c
update psims version in mzml metadata
gtluu Sep 29, 2023
faa2502
Merge branch 'main' of https://github.com/gtluu/timsconvert into depe…
gtluu Sep 29, 2023
7d837f4
add conda environment files for w10 and ubuntu
gtluu Sep 29, 2023
9679506
update requirements and environments
gtluu Sep 29, 2023
e7ad16a
update documentation
gtluu Oct 1, 2023
a895341
update Dockerfile
gtluu Oct 1, 2023
8923d40
Delete meta.yaml
gtluu Oct 1, 2023
879a1ee
Delete environment_ubuntu_dev.yml
gtluu Oct 1, 2023
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3 changes: 1 addition & 2 deletions Dockerfile
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@@ -1,8 +1,7 @@
FROM python:3.7
FROM python:3.11
WORKDIR /app
COPY . /app

RUN pip3 install -r requirements.txt
RUN pip3 install git+https://github.com/gtluu/pyimzML

ENTRYPOINT ["python3", "/app/bin/run.py"]
< 8000 /div>
10 changes: 5 additions & 5 deletions docs/_sources/installation.rst.txt
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Expand Up @@ -11,11 +11,11 @@ Installing on Windows

3. Run ``Anaconda Prompt``.

4. Create a conda instance. You must be using Python 3.7. Newer versions of Python are not guaranteed to be compatible with Bruker's API in Linux.
4. Create a conda instance.

.. code-block::

conda create -n timsconvert python=3.7
conda create -n timsconvert python=3.11

5. Activate conda environment.

Expand Down Expand Up @@ -50,7 +50,7 @@ LTS. We recommend using this distro if you encounter compatibility issues in oth

wget https://repo.anaconda.com/archive/Anaconda3-2023.07-2-Linux-x86_64.sh

2. If not already installed, install ``git``. On Ubuntu 22.04 LTS, this can be done using the following command.
2. If not already installed, install ``git``. On Ubuntu 22.04.3 LTS, this can be done using the following command.

.. code-block::

Expand All @@ -62,11 +62,11 @@ LTS. We recommend using this distro if you encounter compatibility issues in oth

bash [path to]/Anaconda3-2023.07-2-Linux-x86_64.sh

3. In the terminal, create a conda virtual environment. You must be using Python 3.7. Newer versions of Python are not guaranteed to be compatible with Bruker's API in Linux.
3. In the terminal, create a conda virtual environment.

.. code-block::

conda create -n timsconvert python=3.7
conda create -n timsconvert python=3.11

4. Activate conda environment.

Expand Down
24 changes: 22 additions & 2 deletions docs/_sources/local.rst.txt
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Expand Up @@ -31,8 +31,28 @@ Parameters
.. csv-table::
:file: parameter_descriptions.csv

Notes on ``barebones_metadata parameters`` Parameter
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Notes on ``mode`` Parameter
^^^^^^^^^^^^^^^^^^^^^^^^^^^
There are 3 options for exporting spectra: ``raw``, ``centroid``, and ``profile`` mode. This section describes what
each mode means for different types of raw data.

For ``TSF`` and ``BAF`` files, ``raw`` and ``centroid`` modes are equivalent and will export data in centroid mode.
Note that for ``raw`` mode, all spectra will be labeled as centroided. For these file types, ``profile`` mode is also
as described and will export spectra in profile mode.

For ``TDF`` files in which the data is exported without writing out the ion mobility binary arrays, ``raw`` mode
exports centroided spectra using the ``tims_read_scans_v2`` function from Bruker's ``TDF-SDK``. Note that as mentioned
above, all spectra will be labeled as centroided. ``centroid`` mode exports centroided spectra using a different
function, ``tims_extract_centroided_spectrum_for_frame_v2`` function from ``TDF-SDK``. This results in minor
differences in the resulting line spectra, but most major peaks should be equivalent. For ``profile`` mode ``TDF``
files, the ``tims_extract_profile_for_frame`` function is used to extract a quasi-profile spectrum from the raw data.

For ``TDF`` files in which the data is exported with the ion mobiilty arrays (resulting in 3 binary data arrays for
m/z, intensity, and ion mobility, only ``raw`` mode is available due to conversion speed and the resulting data size if
``centroid`` or ``profile`` mode are used. Again, all spectra are labeled as centroided.

Notes on ``barebones_metadata` Parameter
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If the ``--barebones_metadata`` flag is used when running TIMSCONVERT, the following metadata is not written to the
resulting mzML file: 1) software list including acquistion and data conversion software, 2) data processing list
including data conversion software, and 3) instrument name. This is done to allow for compatibility with older software
Expand Down
11 changes: 6 additions & 5 deletions docs/installation.html
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Expand Up @@ -45,8 +45,8 @@ <h2>Installing on Windows<a class="headerlink" href="#installing-on-windows" tit
<li><p>Download and install <a class="reference external" href="https://repo.anaconda.com/archive/Anaconda3-2023.07-2-Windows-x86_64.exe">Anaconda for Windows</a> if not already installed. Follow the prompts to complete installation.</p></li>
<li><p>Download and install <a class="reference external" href="https://github.com/git-for-windows/git/releases/download/v2.42.0.windows.2/Git-2.42.0.2-64-bit.exe">Git for Windows</a> if not already installed.</p></li>
<li><p>Run <code class="docutils literal notranslate"><span class="pre">Anaconda</span> <span class="pre">Prompt</span></code>.</p></li>
<li><p>Create a conda instance. You must be using Python 3.7. Newer versions of Python are not guaranteed to be compatible with Bruker’s API in Linux.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">create</span> <span class="o">-</span><span class="n">n</span> <span class="n">timsconvert</span> <span class="n">python</span><span class="o">=</span><span class="mf">3.7</span>
<li><p>Create a conda instance.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">create</span> <span class="o">-</span><span class="n">n</span> <span class="n">timsconvert</span> <span class="n">python</span><span class="o">=</span><span class="mf">3.11</span>
</pre></div>
</div>
</li>
Expand Down Expand Up @@ -81,7 +81,7 @@ <h2>Installing on Linux<a class="headerlink" href="#installing-on-linux" title="
</pre></div>
</div>
</li>
<li><p>If not already installed, install <code class="docutils literal notranslate"><span class="pre">git</span></code>. On Ubuntu 22.04 LTS, this can be done using the following command.</p>
<li><p>If not already installed, install <code class="docutils literal notranslate"><span class="pre">git</span></code>. On Ubuntu 22.04.3 LTS, this can be done using the following command.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">apt</span><span class="o">-</span><span class="n">get</span> <span class="n">install</span> <span class="n">git</span>
</pre></div>
</div>
Expand All @@ -93,8 +93,8 @@ <h2>Installing on Linux<a class="headerlink" href="#installing-on-linux" title="
</pre></div>
</div>
</li>
<li><p>In the terminal, create a conda virtual environment. You must be using Python 3.7. Newer versions of Python are not guaranteed to be compatible with Bruker’s API in Linux.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">create</span> <span class="o">-</span><span class="n">n</span> <span class="n">timsconvert</span> <span class="n">python</span><span class="o">=</span><span class="mf">3.7</span>
<li><p>In the terminal, create a conda virtual environment.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">create</span> <span class="o">-</span><span class="n">n</span> <span class="n">timsconvert</span> <span class="n">python</span><span class="o">=</span><span clas 9E12 s="mf">3.11</span>
</pre></div>
</div>
</li>
Expand Down Expand Up @@ -147,6 +147,7 @@ <h3>Navigation</h3>
<li class="toctree-l1"><a class="reference internal" href="gnps.html">GNPS Usage</a></li>
<li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
<li class="toctree-l1"><a class="reference internal" href="timsconvert.html">TIMSCONVERT Source Code</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Modules</a></li>
</ul>

<div class="relations">
Expand Down
21 changes: 19 additions & 2 deletions docs/local.html
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Expand Up @@ -114,8 +114,25 @@ <h2>Parameters<a class="headerlink" href="#parameters" title="Permalink to this
</tr>
</tbody>
</table>
<section id="notes-on-barebones-metadata-parameters-parameter">
<h3>Notes on <code class="docutils literal notranslate"><span class="pre">barebones_metadata</span> <span class="pre">parameters</span></code> Parameter<a class="headerlink" href="#notes-on-barebones-metadata-parameters-parameter" title="Permalink to this heading">¶</a></h3>
<section id="notes-on-mode-parameter">
<h3>Notes on <code class="docutils literal notranslate"><span class="pre">mode</span></code> Parameter<a class="headerlink" href="#notes-on-mode-parameter" title="Permalink to this heading">¶</a></h3>
<p>There are 3 options for exporting spectra: <code class="docutils literal notranslate"><span class="pre">raw</span></code>, <code class="docutils literal notranslate"><span class="pre">centroid</span></code>, and <code class="docutils literal notranslate"><span class="pre">profile</span></code> mode. This section describes what
each mode means for different types of raw data.</p>
<p>For <code class="docutils literal notranslate"><span class="pre">TSF</span></code> and <code class="docutils literal notranslate"><span class="pre">BAF</span></code> files, <code class="docutils literal notranslate"><span class="pre">raw</span></code> and <code class="docutils literal notranslate"><span class="pre">centroid</span></code> modes are equivalent and will export data in centroid mode.
Note that for <code class="docutils literal notranslate"><span class="pre">raw</span></code> mode, all spectra will be labeled as centroided. For these file types, <code class="docutils literal notranslate"><span class="pre">profile</span></code> mode is also
as described and will export spectra in profile mode.</p>
<p>For <code class="docutils literal notranslate"><span class="pre">TDF</span></code> files in which the data is exported without writing out the ion mobility binary arrays, <code class="docutils literal notranslate"><span class="pre">raw</span></code> mode
exports centroided spectra using the <code class="docutils literal notranslate"><span class="pre">tims_read_scans_v2</span></code> function from Bruker’s <code class="docutils literal notranslate"><span class="pre">TDF-SDK</span></code>. Note that as mentioned
above, all spectra will be labeled as centroided. <code class="docutils literal notranslate"><span class="pre">centroid</span></code> mode exports centroided spectra using a different
function, <code class="docutils literal notranslate"><span class="pre">tims_extract_centroided_spectrum_for_frame_v2</span></code> function from <code class="docutils literal notranslate"><span class="pre">TDF-SDK</span></code>. This results in minor
differences in the resulting line spectra, but most major peaks should be equivalent. For <code class="docutils literal notranslate"><span class="pre">profile</span></code> mode <code class="docutils literal notranslate"><span class="pre">TDF</span></code>
files, the <code class="docutils literal notranslate"><span class="pre">tims_extract_profile_for_frame</span></code> function is used to extract a quasi-profile spectrum from the raw data.</p>
<p>For <code class="docutils literal notranslate"><span class="pre">TDF</span></code> files in which the data is exported with the ion mobiilty arrays (resulting in 3 binary data arrays for
m/z, intensity, and ion mobility, only <code class="docutils literal notranslate"><span class="pre">raw</span></code> mode is available due to conversion speed and the resulting data size if
<code class="docutils literal notranslate"><span class="pre">centroid</span></code> or <code class="docutils literal notranslate"><span class="pre">profile</span></code> mode are used. Again, all spectra are labeled as centroided.</p>
</section>
<section id="notes-on-barebones-metadata-parameter">
<h3>Notes on <a href="#id1"><span class="problematic" id="id2">``</span></a>barebones_metadata` Parameter<a class="headerlink" href="#notes-on-barebones-metadata-parameter" title="Permalink to this heading">¶</a></h3>
<p>If the <code class="docutils literal notranslate"><span class="pre">--barebones_metadata</span></code> flag is used when running TIMSCONVERT, the following metadata is not written to the
resulting mzML file: 1) software list including acquistion and data conversion software, 2) data processing list
including data conversion software, and 3) instrument name. This is done to allow for compatibility with older software
Expand Down
8 changes: 7 additions & 1 deletion docs/modules.html
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Expand Up @@ -17,6 +17,7 @@
<script src="_static/sphinx_highlight.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="prev" title="timsconvert package" href="timsconvert.html" />

<link rel="stylesheet" href="_static/custom.css" type="text/css" />

Expand Down Expand Up @@ -138,19 +139,24 @@ <h1 class="logo"><a href="index.html">TIMSCONVERT</a></h1>

<h3>Navigation</h3>
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="local.html">Local Usage</a></li>
<li class="toctree-l1"><a class="reference internal" href="gnps.html">GNPS Usage</a></li>
<li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
<li class="toctree-l1"><a class="reference internal" href="timsconvert.html">TIMSCONVERT Source Code</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Modules</a><ul>
<li class="toctree-l2"><a class="reference internal" href="timsconvert.html">timsconvert package</a></li>
</ul>
</li>
</ul>

<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
<li>Previous: <a href="timsconvert.html" title="previous chapter">timsconvert package</a></li>
</ul></li>
</ul>
</div>
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<script src="_static/sphinx_highlight.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="timsconvert" href="modules.html" />
<link rel="prev" title="Advanced Usage" href="advanced.html" />

<link rel="stylesheet" href="_static/custom.css" type="text/css" />
Expand Down Expand Up @@ -1132,13 +1133,15 @@ <h3>Navigation</h3>
<li class="toctree-l2"><a class="reference internal" href="#module-timsconvert">Module contents</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Modules</a></li>
</ul>

<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
<li>Previous: <a href="advanced.html" title="previous chapter">Advanced Usage</a></li>
<li>Next: <a href="modules.html" title="next chapter">timsconvert</a></li>
</ul></li>
</ul>
</div>
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10 changes: 5 additions & 5 deletions docsrc/build/html/_sources/installation.rst.txt
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Expand Up @@ -11,11 +11,11 @@ Installing on Windows

3. Run ``Anaconda Prompt``.

4. Create a conda instance. You must be using Python 3.7. Newer versions of Python are not guaranteed to be compatible with Bruker's API in Linux.
4. Create a conda instance.

.. code-block::

conda create -n timsconvert python=3.7
conda create -n timsconvert python=3.11

5. Activate conda environment.

Expand Down Expand Up @@ -50,7 +50,7 @@ LTS. We recommend using this distro if you encounter compatibility issues in oth

wget https://repo.anaconda.com/archive/Anaconda3-2023.07-2-Linux-x86_64.sh

2. If not already installed, install ``git``. On Ubuntu 22.04 LTS, this can be done using the following command.
2. If not already installed, install ``git``. On Ubuntu 22.04.3 LTS, this can be done using the following command.

.. code-block::

Expand All @@ -62,11 +62,11 @@ LTS. We recommend using this distro if you encounter compatibility issues in oth

bash [path to]/Anaconda3-2023.07-2-Linux-x86_64.sh

3. In the terminal, create a conda virtual environment. You must be using Python 3.7. Newer versions of Python are not guaranteed to be compatible with Bruker's API in Linux.
3. In the terminal, create a conda virtual environment.

.. code-block::

conda create -n timsconvert python=3.7
conda create -n timsconvert python=3.11

4. Activate conda environment.

Expand Down
24 changes: 22 additions & 2 deletions docsrc/build/html/_sources/local.rst.txt
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Expand Up @@ -31,8 +31,28 @@ Parameters
.. csv-table::
:file: parameter_descriptions.csv

Notes on ``barebones_metadata parameters`` Parameter
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Notes on ``mode`` Parameter
^^^^^^^^^^^^^^^^^^^^^^^^^^^
There are 3 options for exporting spectra: ``raw``, ``centroid``, and ``profile`` mode. This section describes what
each mode means for different types of raw data.

For ``TSF`` and ``BAF`` files, ``raw`` and ``centroid`` modes are equivalent and will export data in centroid mode.
Note that for ``raw`` mode, all spectra will be labeled as centroided. For these file types, ``profile`` mode is also
as described and will export spectra in profile mode.

For ``TDF`` files in which the data is exported without writing out the ion mobility binary arrays, ``raw`` mode
exports centroided spectra using the ``tims_read_scans_v2`` function from Bruker's ``TDF-SDK``. Note that as mentioned
above, all spectra will be labeled as centroided. ``centroid`` mode exports centroided spectra using a different
function, ``tims_extract_centroided_spectrum_for_frame_v2`` function from ``TDF-SDK``. This results in minor
differences in the resulting line spectra, but most major peaks should be equivalent. For ``profile`` mode ``TDF``
files, the ``tims_extract_profile_for_frame`` function is used to extract a quasi-profile spectrum from the raw data.

For ``TDF`` files in which the data is exported with the ion mobiilty arrays (resulting in 3 binary data arrays for
m/z, intensity, and ion mobility, only ``raw`` mode is available due to conversion speed and the resulting data size if
``centroid`` or ``profile`` mode are used. Again, all spectra are labeled as centroided.

Notes on ``barebones_metadata` Parameter
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If the ``--barebones_metadata`` flag is used when running TIMSCONVERT, the following metadata is not written to the
resulting mzML file: 1) software list including acquistion and data conversion software, 2) data processing list
including data conversion software, and 3) instrument name. This is done to allow for compatibility with older software
Expand Down
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