fmihpc · alhom · Feb 4, 2025 · Dec 15, 2024 · Dec 15, 2024 · Dec 15, 2024
diff --git a/.github/workflows/test_python.yml b/.github/workflows/test_python.yml
@@ -33,7 +33,7 @@ jobs:
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         python -m pip install numpy scipy matplotlib scikit-image # add versions to matrix
     - name: Trial imports
-      run: python -c 'import pytools as pt'
+      run: python -c 'import analysator as pt'
 
   ubuntu_22_04_versions:
 
@@ -57,7 +57,7 @@ jobs:
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         python -m pip install numpy scipy matplotlib scikit-image # add versions to matrix
     - name: Trial imports
-      run: python -c 'import pytools as pt'
+      run: python -c 'import analysator as pt'
 
 
   lint:

diff --git a/Documentation/components/mayavi/mayavi_usage.tex b/Documentation/components/mayavi/mayavi_usage.tex
@@ -71,7 +71,7 @@
 \section{Plotting the grid}
 
 \begin{python}
-import pytools as pt
+import analysator as pt
 f = pt.vlsvfile.VlsvReader('bulk.0000872.vlsv')
 grid = pt.grid.MayaviGrid(f, 'rho')
 \end{python}

diff --git a/Documentation/examples/example1.py b/Documentation/examples/example1.py
@@ -21,7 +21,7 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 # 
 
-import pytools as pt
+import analysator as pt
 
 f = pt.vlsvfile.VlasiatorReader('fullf.0000002.vlsv')
 grid = pt.grid.Particlepusherinterface(f, 'rho')

diff --git a/Documentation/installation/installation.tex b/Documentation/installation/installation.tex
@@ -46,7 +46,7 @@ \section{Testing installation}
 \begin{verbatim}
 cd ~/analysator
 ipython
-import pytools as pt
+import analysator as pt
 \end{verbatim}
 
 The full input/output should look like this (if the installation fails, the import command should 
@@ -63,7 +63,7 @@ \section{Testing installation}
 help      -> Python's own help system.
 object?   -> Details about 'object', use 'object??' for extra details.
 
-In [1]: import pytools as pt
+In [1]: import analysator as pt
 
 In [2]: 
 

diff --git a/Documentation/particle_pusher/particlepusher.tex b/Documentation/particle_pusher/particlepusher.tex
@@ -34,7 +34,7 @@ \section{Using the particle pusher interface}
 \begin{verbatim}
 ipython
 
-In [2]: import pytools as pt
+In [2]: import analysator as pt
 
 In [3]: f = pt.vlsvfile.VlasiatorReader('bulk.0001480.vlsv')
 

diff --git a/Documentation/presentations/analysator.tex b/Documentation/presentations/analysator.tex
@@ -111,7 +111,7 @@ \section{Introduction}
  \begin{python}[basicstyle=\tiny]
   # We are interested in reading data from the cell whose ID is 75
 
-  import pytools as pt # Import Analysator
+  import analysator as pt # Import Analysator
 
   # Open a vlsv file for reading
   vlsvReader = pt.vlsvfile.VlsvReader('bulk.0003710.vlsv')
@@ -163,7 +163,7 @@ \section{Concepts}
 
  \begin{python}[basicstyle=\tiny]
   # Import analysator
-  import pytools as pt
+  import analysator as pt
 
   vlsvReader = pt.vlsvfile.VlsvReader('test.vlsv') #What?
 
@@ -189,7 +189,7 @@ \section{Concepts}
  \frametitle{Navigation (the \emph{most} important part)}
  \begin{python}[basicstyle=\tiny]
   # Import analysator
-  import pytools as pt
+  import analysator as pt
 
   pt.
  \end{python}
@@ -205,7 +205,7 @@ \section{Concepts}
  \frametitle{Navigation (the \emph{most} important part)}
  \begin{python}[basicstyle=\tiny]
   # Import analysator
-  import pytools as pt
+  import analysator as pt
 
   pt.calculations.
  \end{python}
@@ -227,7 +227,7 @@ \section{Concepts}
  \frametitle{Navigation (the \emph{most} important part)}
  \begin{python}[basicstyle=\tiny]
   # Import analysator
-  import pytools as pt
+  import analysator as pt
 
   pt.calculations.cut_through?
  \end{python}
@@ -287,7 +287,7 @@ \section{Basics}
  \frametitle{Basic usage}
  \begin{python}[basicstyle=\tiny]
   # Import analysator
-  import pytools as pt
+  import analysator as pt
 
   # Open a vlsv file
   vlsvReader = pt.vlsvfile.VlsvReader('test.vlsv')
@@ -384,7 +384,7 @@ \section{Plotting}
  Plotting can be done simply by feeding a vlsv file to the grid class as follows:
  \begin{python}[basicstyle=\tiny]
   # Import Analysator
-  import pytools as pt
+  import analysator as pt
 
   # Open a vlsv file
   vlsvReader = pt.vlsvfile.VlsvReader('test.vlsv')
@@ -532,7 +532,7 @@ \section{Hands-on}
  \frametitle{Example from \emph{calculations}}
  \begin{python}[basicstyle=\tiny]
   # Import analysator
-  import pytools as pt
+  import analysator as pt
 
   # Open a vlsv file
   vlsvReader = pt.vlsvfile.vlsvReader('testfile.vlsv')

diff --git a/Documentation/sphinx/calculations.rst b/Documentation/sphinx/calculations.rst
@@ -1,6 +1,6 @@
 calculations
 =================================
 
-.. automodule:: pytools.calculations
+.. automodule:: analysator.calculations
    :members:
    :imported-members:
diff --git a/Documentation/sphinx/conf.py b/Documentation/sphinx/conf.py
@@ -11,7 +11,7 @@
 
 sys.path.insert(0, str(Path('..', '..').resolve()))
 sys.path.insert(0, str(Path('..', '..', 'scripts').resolve()))
-print(str(Path('..','..').resolve()))
+print(str(Path('..','..','analysator').resolve()))
 print(str(Path('..','..', 'scripts').resolve()))
 project = 'analysator'
 copyright = '2024, University of Helsinki'
@@ -32,7 +32,7 @@
     pass
 
 
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'pytools']
 
 
 

diff --git a/Documentation/sphinx/fetchscripts.py b/Documentation/sphinx/fetchscripts.py
@@ -1,7 +1,7 @@
 import glob
 import os
 
-files = glob.glob('C:/Users/samel/OneDrive/Tiedostot/TET/analysator/scripts/*.py')
+files = glob.glob('../scripts/*.py')
 
 for file in files:
     file = os.path.basename(file)[:-3]

diff --git a/Documentation/sphinx/index.rst b/Documentation/sphinx/index.rst
@@ -33,7 +33,7 @@ documentation for details.
    scripts
    about
 
-.. automodule:: pytools 
+.. automodule:: analysator 
    :members:
    :imported-members:
    :undoc-members:

diff --git a/Documentation/sphinx/miscellaneous.rst b/Documentation/sphinx/miscellaneous.rst
@@ -1,6 +1,6 @@
 miscellaneous
 ==================================
 
-.. automodule:: pytools.miscellaneous
+.. automodule:: miscellaneous
    :members:
    :imported-members:
diff --git a/Documentation/sphinx/plot.rst b/Documentation/sphinx/plot.rst
@@ -1,7 +1,7 @@
 plot
 ============================
 
-.. automodule:: pytools.plot
+.. automodule:: analysator.plot
    :members:
    :exclude-members: Version
    :imported-members:

diff --git a/Documentation/sphinx/vlsvfile.rst b/Documentation/sphinx/vlsvfile.rst
@@ -3,6 +3,6 @@ vlsvfile
 
 VlsvFile is responsibe for implementing read and write functionality for the vlsv format, as well as defining data reducers and reduction pipelines. Some of this will be likely moved around to be more modular in some indefinite point in the future.
 
-.. automodule:: pytools.vlsvfile
+.. automodule:: analysator.vlsvfile
    :members:
    :imported-members:
diff --git a/README b/README
diff --git a/README.md b/README.md
@@ -0,0 +1,71 @@
+# Installation:
+
+Analysator is now a package! Clone the repository locally
+
+```bash
+git clone https://github.com/fmihpc/analysator.git
+```
+and install via `pip` from the cloned path. Dependency handling is via pip. Using the editable flag is recommended for getting updates via `git pull origin`:
+
+```bash
+pip install -e ./analysator
+```
+
+## Backward compatibility
+
+The packaged analysator is (should be!) backwards-compatible with previous analysator versions: `import pytools` will import analysator onto the pytools name, and emits a deprecation warning. `$PYTHONPATH` installation is also supported.
+
+# Using Analysator:
+```python
+import analysator as pt  # Import Analysator
+
+# Navigating functions:
+pt.calculations.pitch_angles? #press [Enter]
+pt.vlsvfile.VlsvReader? #press [Enter]
+pt.plot.plot_colormap? #press [Enter]
+pt.plot.plot_vdf? #press [Enter]
+```
+
+```bash
+# For non-interactive mode (also when no X is available):
+# set the environment variable PTNONINTERACTIVE to any value before launching
+# python/ipython. If in interactive mode, experimental non-blocking
+# windows via matplotlib.pyplot.ion() are in use.
+#################################################
+export PTNONINTERACTIVE=1
+
+# For selecting a backend manually (if Agg or TkAgg is not available)
+#################################################
+export PTBACKEND=Qt5Agg
+
+# For disabling full LaTeX formatted output (if texlive is not installed)
+#################################################
+export PTNOLATEX=1
+```
+
+# Outputs
+
+For setting the default output directory (default: $HOME/Plots)
+```
+export PTOUTPUTDIR=/proj/USERNAME/Plots/
+```
+If using a jupyter notebook on the UH hub system, you can activate interactive plot windows with `%matplotlib ipympl` or `%matplotlib notebook` before importing pytools
+
+Examples and instructions for batch scripting (on CSC's system) are found in
+`examples/generate_panel.py` and `examples/generate_movie.sh`
+
+Analysator is using logging. It is controlled by setting the enviroment variable ANALYSATOR_LOG_LEVEL
+Supported: DEBUG, INFO (default), WARNING, ERROR, CRITICAL
+
+For example, disable INFO prints via:
+```bash
+export ANALYSATOR_LOG_LEVEL='WARNING'
+```
+
+# About
+
+For more information visit the wiki: https://github.com/fmihpc/analysator/wiki
+
+Analysator reference: https://fmihpc.github.io/analysator/
+
+For citations, use the DOI https://doi.org/10.5281/zenodo.4462514 or the ready-made button the the right in GitHub!